Disobeying team orders and a pre-race agreement, the German snatched the lead from Webber, who had "turned the engine down" in the run to the flag, despite instructions and protests from the pitwall.
Practice and Qualifying
Red Bull, Mercedes and Lotus were the cars to watch in practice, with Ferrari, like the weather, threatening.
Qualifying was spoiled by a heavy shower for the final ten minute session, forcing the drivers to qualify with intermediate tyres.
Vettel did a run, returned for new tyres and went out again, earning him pole. The Ferraris sprung a surprise with second and third, Hamilton close behind.
Raikkonen was knocked back three places to seventh after it was decided he had impeded Rosberg, promoting Webber one place to fifth.
The race was preceded by a torrential downpour that lasted about half an hour, but the effects lasted until well after the lights went out.
Several drivers fell off the road on their way to form up on the grid, underlining how wet it was. The whole grid started on intermediates.
Webber got a fantastic start, streaking through to third behind Alonso, who lost his front wing to Sebastien Vettel's rear tyre, but it didn't quite come off. Alonso carried on to the second lap, failing to pit and blocking a tentative Webber from getting by.
As Webber passed him on the straight on the way to turn one, the wing failed completely, dropping under Alonso's front wheels, rendering him a passenger.
Webber took the corner ahead of Alonso, narrowly missing being cleaned up by the stricken Ferrari.
Button and Rosberg started a very entertaining battle for fourth after the McLaren driver had got an excellent start. Rosberg prevailed despite Button's canny moves, the Briton holding the position for half the race.
Championship leader Raikkonen ended up behind Daniel Ricciardo, the Lotus struggling on the intermediates, the Toro Rosso revelling.
Sauber's Hulkenberg muscled his way to seventh by the end of lap five, passing Perez's McLaren.
Vettel pitted for slicks on lap six, as did Massa, with the rest of the field following suit the next lap. Melbourne hero Sutil had a terrible stop, the Force India's left rear sticking.
Webber pitted a lap later than Vettel and emerged ahead. In an unusual turn of events, Webber was told in a coded message that he was safe from attack.
Lewis Hamilton pitted on lap 7 and had to be waved through the McLaren pit. The blunder didn't hurt too badly, the Brit hanging on to third place ahead of teammate Rosberg.
Further down pit lane, Jean-Eric Vergne was released into the path of Pic's Caterham, the two coming together and knocking Vergne's front wing off.
Back in the midfield, Toro Rosso's Ricciardo held off Raikkoneon for a couple of laps before being passed by the Finn.
By lap 10, Webber held a three-second lead over Vettel on the hard tyre, the German on the medium compound.
As the track dried out, Webber was reeled in by Vettel who himself was being caught by both Mercedes cars for a few laps, before stabilising the gap.
Pastor Maldonado threw his Williams off the track on lap 14, breaking his front wing but was able to regain the track after bouncing through the gravel. He did it again towards the end of the race but was unable to continue.
Raikkonen was by now back up to tenth, but resolutely stuck behind a hard defending Perez, while Grosjean drove away. Raikkonen finally passed the Mexican on lap 16 with the aid of DRS and went on to set the fastest lap of the race thus far.
Massa's front row start was a bitter memory, the Ferrari driver having slid to seventh after his pit stops.
Webber pitted at end of lap 19, a lightning fast stop for softer medium compound tyres, Ricciardo doing the same from 11th after being passed by di Resta.
Vettel took to having the lead with gusto, setting a quick lap to try and leap Webber in his pit stop. Massa came in on lap 21, with Grosjean close behind.
di Resta pitted and was stuck for many seconds with a problem on his left front. While he sat there, Hamilton came in, this time without incident.
Jenson Button, also pitted as did Raikkonen. The problem eventually ended di Resta's race.
Vettel pitted and came out behind Webber, still around 2.5 seconds adrift despite his heroic efforts.
Sutil again had terrible trouble in his pit stop, with his front left sticking. His race would end in the garage too.
Vettel began closing on Webber on lap 25 as both Mercedes attacked again, the Red Bulls looking after their tyres to optimise their strategy.
The team radioed their champion driver to ease off, but this had no obvious effect. Webber was then asked to pick up a few tenths.
Vettel then fired back to tell the team to get the Australian to get out of the way. Webber responded by pulling out a 1.6 second lead to get Vettel out of the DRS zone.
Webber pitted on lap 32 and he went back out on his favoured tyre, the hard compound Pirelli. The Australian got out ahead of the lapped traffic of Pic and van der Garde.
Vettel pitted the following lap and went back on to mediums. It cost him dearly as the Mercedes strategy worked, putting Hamilton in front and Rosberg right behind him.
Jenson Button then enjoyed the lead of the race for a few laps before Webber unsuccessfully tried to pass him at turn one to liven things up.
Button then pitted on lap 36 for hard compound tyres. He was then stranded in pit lane, the McLaren team taking a while to respond and push him back down the lane.
Replays showed the McLaren was released before the right front gunman was finished. He would later retire, although consoled by the pace of his McLaren.
Webber's lead quickly extended to almost four seconds while Vettel battled the Mercedes cars. Hamilton's team insisted he conserve fuel and he soon lost second to an impatient Vettel.
Hamilton pitted for the last time on lap 42, bringing his total to four stops, meaning he needed to make the medium compound last 14 laps.
Vettel pitted on lap 43 for his fourth stop, followed by Rosberg. Both took on mediums and left the lane in the same order. The big loser was Hamilton, jumped by his teammate in that stop.
Webber pitted a lap later, for yet another set of hard tyres. This precipitated an epic battle with Vettel, the team frantically telling the German to be careful.
Despite the DRS advantage, Vettel was unable to pass into turn one, while behind him Hamilton was able to get by Rosberg into the final hairpin.
The Vettel-Webber fight continued ahead of the Mercedes' who were also battling. Vettel nearly ended up on the grass on the main straight, playing Russian roulette with his teammate by going down the inside.
Webber held the place for a few more corners, losing out on the marbles at turn four.
It transpired that Vettel not only ignored team orders but a pre-race agreement. Webber was suitably incensed.
As with Red Bull, the two drivers were squabbling over position, with Rosberg arguing with team principal Brawn over the radio, but told to hold station behind Hamilton who himself had been told to stay on a target lap time.
The German wasn't pleased and pleaded his case again several laps later and was again rebuffed.
A downcast Hamilton said after the race that third should have been Rosberg's.
Daniel Ricciardo's promising race ended on lap 53 as he pulled into the pits to retire.
Vettel took the flag and weaved ecstatically in front of his pit, while Webber pointedly crossed to the opposite side of track. The pitwall looked rather less pleased than Vettel, who later said he misunderstood the orders and passed by mistake.
The radio message to Vettel was loaded: "Good job, Seb. Looks like you wanted it bad enough. Still you've got some explaining to do," Christian Horner said.
The argument spilled over into the driver's room, with Vettel first arguing with Adrian Newey and then Webber himself who strode in some time after Vettel and Hamilton. There followed a very tense podium presentation and press conference.
"After the last stop the team told me the race was over and we turned the engine down to go to the end," said Webber.
"I want to race as well, but in the end the team made a decision which we always say before the start of the race is how it's probably going to be."
"In the end Seb made his own decisions today and will have protection as usual, and that's the way it goes."
Formula 1 returns for the Chinese Grand Prix in three weeks.
2013 Malaysian F1 GP Results
- Vettel - Red Bull-Renault
- Webber - Red Bull-Renault + 4.298
- Hamilton - Mercedes + 12.1
- Rosberg - Mercedes + 12.640
- Massa - Ferrari + 25.6
- Grosjean - Lotus-Renault + 35.5
- Raikkonen - Lotus-Renault + 48.4
- Hulkenberg - Sauber-Ferrari + 53.0
- Perez - McLaren-Mercedes + 72.3
- Vergne - Toro Rosso-Ferrari + 87.1
- Bottas - Williams-Renault + 88.6
- Gutierrez - Sauber-Ferrari + 1 lap
- Bianchi - Marussia-Cosworth + 1 lap
- Pic - Caterham-Renault + 1 lap
- van der Garde - Caterham-Renault + 1 lap
- Chilton - Marussia-Cosworth + 2 laps
- Button - McLaren-Mercedes + 2 laps
- Ricciardo - Toro Rosso-Ferrar + 2 laps
- Maldonado - Williams-Renault
- Sutil - Force India-Mercedes
- Di Resta - Force India-Mercedes
- Alonso - Ferrari
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