The holding midfielder is seen as one of Germany's most talented youngsters and will be looking to gain valuable first-team action at his new club.
The midfielder, 19, was keen to leave the Allianz Arena due to the stiff competition for places at the club and will now continue his career at the BayArena after signing a four-year deal with the Werkself.
"Bayer Leverkusen are one of the top teams in the Bundesliga and play in the Champions League as well. I want to play my part in helping the team to success in each competition they compete in in the years to come," Can said.
Bayern have an option to re-sign the Germany Under-21 international for a set fee at some point in the future, and chairman Karl-Heinz Rummenigge feels joining Leverkusen is the right move for Can at this stage of his career.
"Emre Can is one of the biggest talents in German football. We’ve taken this step to ensure he gains sufficient match practice, as we’ve done in the past with the likes of Toni Kroos at Leverkusen, Philipp Lahm with Stuttgart and David Alaba at Hoffenheim," Rummenigge said.
Can made his official Bayern debut in the 2012 DFL Supercup, but he has since failed to secure regular first-team action for the Bavarians.