The Brazil international has signed a three-year deal that will keep him at Bayern Munich until the summer of 2014.
The 25-year-old joins Bayern in a deal reportedly worth €5.5million from Italian side Genoa.
Rafinha said: “I’m delighted the move to FC Bayern has worked out and that I’ll be able to play in the Bundesliga again.”
Bayern sporting director Christian Nerlinger said: “With Rafinha we’ve signed a tried-and-tested player who will further stabilise our defence and benefit the development of the team as a whole.
“We’re very happy to have been able to agree terms with both him and Genoa on a move to Munich.”