Details of the agreement have not been revealed, with DRB confirming only that Honda will become a "strategic partner" in a program that will see Proton, and its Lotus sports car arm, evolve as "an original equipment manufacturer".
It has been reported that the deal could see collaboration on new technologies and platforms, making the brands more competitive in a market where shared architectures have become commonplace.
The deal will not involve an equity stake however, suggesting the partnership may be limited to shared production facilities rather than co-developed technologies.
For Proton, the deal follows unsuccessful talks over the past year with both Volkswagen and PSA Peugeot Citroen.
While the Proton brand has struggled to make inroads in the global market, Honda has not been without troubles of its own.
Last year's devastating Thailand floods drastically affected the carmaker's manufacturing, and the China/Japan territorial disputes have caused the brand to cut its Chinese-market sales targets.
The deal will likely also see Honda boost production in Malaysia, where it currently builds the midsized CR-V SUV.