Jenson Button streaked to his first pole position since 2009, his first for McLaren in fifty races with the British team.
Red Bull were way off the pace, not helped by Webber's grid penalty, pushing Sauber and Williams to grid slots you would normally expect to see Red Bulls or McLarens occupy.
After a wet Friday, Saturday's sessions were a compressed program for the teams as they tried to cram in the work usually done on Friday.
Friday practice was held in utterly terrible conditions, the drivers choosing to stay dry for the most part. One driver who didn't, Kamui Kobayashi, took the top slot in first practice.
Second practice was even more desolate, with Charles Pic topping the times and Daniel Ricciardo running second behind him.
Despite a lack of running, there was a small amount of drama - Felipe Massa's engine expired as he splashed his way around the forest circuit. Mark Webber's gearbox had to be changed and he copped a five place grid penalty.
Saturday morning's Free Practice 3 was a frantic affair as the teams tried desperately to set the cars up for dry running.
Fernando Alonso's declaration earlier in the week that his Ferrari was the slowest-of-the-fast cars looked ever more ludicrous as he went fastest, with the Lotus of Kimi Raikkonen and both Saubers behind.
Mark Webber ran seventh, six-tenths off Alonso's time and Vettel ninth, a further tenth back. Daniel Ricciardo was on his teammate's tail in 16th.
Nico Rosberg suffered the same fate as Mark Webber after his car coasted to a halt, a gearbox problem stopping his Mercedes and handing him a five-place penalty.
Lotus team boss Eric Boullier said before qualifying that the session would come down to a fight between Alonso and Raikkonen.
Rosberg set the first flying lap for Q1 and set the benchmark at 1m51.125s. The time was quickly eclipsed by Saubers, Force Indias, Williamses and Lotuses. All but Webber, Raikkonen and Vettel had set a lap.
By the end of the first half of the session, Perez was still on top with his 1m49.642, with McLaren's Lewis Hamilton behind him. Felipe Massa's Ferrari had terrible understeer, while Alonso went P1 with just over eight minutes to go.
Button radioed to say he was suffering with understeer but he put his car at the top of the timesheets with six minutes to go, just as the Red Bulls and Raikkonen hit the track.
With less than three from the flag, Pastor Maldonado was the first car to dip into the 1m48s range while both Schumacher and Rosberg went out on fresh tyres to stay in the game. Rosberg failed to improve his time as the flag fell but his veteran teammate did.
Q2 was busy from the first moment, with almost the entire field taking to the 7km track, with just Button and Senna remaining pit-bound.
Perez laid down the challenge to the field with a 1m48.880s. Webber bettered it about a minute later by just over two-tenths. Alonso then took the top slot by just a few hundredths.
Despite an indiscretion through the Bus Stop chicane, Hamilton went first and was then deposed by Raikkonen seconds later.
Jenson Button smashed Raikkonen's time by nearly a second while Bruno Senna threw his car off the road to try and improve from 17th.
Ricciardo, who had been sixth fastest in Q1 went out with Vettel, Webber, Raikkonen and Alonso, all on the softer, medium compound. With just over two minutes left in the session each were leaving themselves time for one flying lap.
Maldonado pushed Felipe Massa from the top ten and Mark Webber went fourth after Perez put in a fantastic final lap.
Sebastien Vettel was a shock departure, beaten by a tenth by Maldonado's Williams.
"I was pretty happy with my lap, it was just not quick enough unfortunately," Vettel said after qualifying.
Michael Schumacher, who had called Spa his 'living room' in the Thursday press conference, was P13 behind Hulkenberg.
Daniel Ricciardo's pace deserted him in Q2, finishing 16th behind Vergne but ahead of Williams' Bruno Senna.
Raikkonen's first flying lap in Q3 yielded a 1m48.2s, which was again completely obliterated by Button a few seconds later. Hamilton pitted after sliding off the road at Rivage, leaving him with little choice but to venture out again.
The Saubers went for a single run in the second half of the ten minute session, as did Alonso and Webber.
The cars cruised around the track like velodrome cyclists, leaving themselves space in front.
Button once more improved on his time as Hamilton set eighth fastest. Mark Webber could only secure seventh.
"Not quick enough for us to challenge for the front row, and that obviously knocks the penalty around a little bit more. I would've liked to have been further up to take the sting off the penalty," Webber said. "The maximum was P5 if I'd got the very most out of it."
Boullier's predicted battle amounted to nothing, with Button, Kobayashi, Maldonado, Raikkonen and Perez separating Alonso from pole.
Maldonado's joy would be short-lived, the Venezuelan handed a three-place penalty for impeding Nico Hulkenberg.
Raikkonen complained of massive understeer, ruing yet another lost opportunity on a track where Lotus were expected to shine.
Webber could only manage seventh, which meant, of course, he would start behind his teammate after serving his penalty. Hamilton set the eighth fastest time and later tweeted that he was running the old rear wing while Jenson had the new, costing Lewis four-tenths on the straights.
Kobayashi and his Sauber team were ecstatic, the Japanese driver starting on the front row for the first time in his Formula 1 career. It was also the first time a Japanese driver had qualified so well since Takuma Sato in 2004.
Button was extremely pleased with his first pole since his lights to flag victory at Monaco in 2009.
"It's been so long since my last pole position that it almost feels like a win for me! In fact, it's my first pole since Monaco 2009 - which was a race that I won – and it demonstrates that I can qualify really well."
1. Jenson Button - McLaren-Mercedes - 1m47.573s
2. Kamui Kobayashi - Sauber-Ferrari - 1m47.871s + 0.298s
3. Pastor Maldonado* - Williams-Renault - 1m47.893s + 0.320s
4. Kimi Raikkonen - Lotus-Renault - 1m48.205s + 0.632s
5. Sergio Perez - Sauber-Ferrari - 1m48.219s + 0.646s
6. Fernando Alonso - Ferrari - 1m48.313s + 0.740s
7. Mark Webber** - Red Bull-Renault - 1m48.392s + 0.819s
8. Lewis Hamilton - McLaren-Mercedes - 1m48.394s + 0.821s
9. Romain Grosjean - Lotus-Renault - 1m48.538s + 0.965s
10. Paul di Resta - Force India-Mercedes - 1m48.890s + 1.317s
11. Sebastian Vettel - Red Bull-Renault
12. Nico Hulkenberg - Force India-Mercedes
13. Michael Schumacher - Mercedes
14. Felipe Massa - Ferrari
15. Jean-Eric Vergne - Toro Rosso-Ferrari
16. Daniel Ricciardo - Toro Rosso-Ferrari
17. Bruno Senna - Williams-Renault
18. Nico Rosberg*** - Mercedes
19. Heikki Kovalainen - Caterham-Renault
20. Vitaly Petrov - Caterham-Renault
21. Timo Glock - Marussia-Cosworth
22. Pedro de la Rosa - HRT-Cosworth
23. Charles Pic - Marussia-Cosworth
24. Narain Karthikeyan - HRT-Cosworth
* Pastor Maldonado will serve a three-place grid penalty for impeding.
** Mark Webber will serve a five-place penalty for a gearbox change.
*** Nico Rosberg will serve a five-place penalty for a gearbox change.