The Germany Under-21 international has signed a four-year deal at the BayArena after being told that he was not part of Pep Guardiola's first-team plans. However, Bayern will retain a buy-back option to buy Can back for an undisclosed fee at a point during the contract.
Can was left out of Bayern's squad for the pre-season Audi Cup tournament, which the German club won by beating Manchester City 2-1 in the final on Thursday.
"Emre Can is a very talented and versatile player," Bayer Leverkusen general manager Rudi Völler told the official Bayer Leverkusen website.
"He will be able to show that at our club in the future. We are happy to have signed him from Bayern Munich."
The player himself also spoke of his happiness at the move.
"Bayer Leverkusen is a top club from Bundesliga 1 and is also playing UEFA Champions League this season," said Can.
"I would like to do my best to help the club have a very successful future in every competition in those future years."