The Peruvian has sealed terms with his former club, where he will act as experienced backup to first-choice centre forward Mario Gomez next season
The 33-year-old's prospective transfer to the Allianz Arena has finally been completed following months of speculation linking the two parties.
A meeting was held in Madrid between the striker's agent Carlos Delgado and sporting director Christian Nerlinger to finalise the deal on Friday, with a medical already undertaken in advance.
"We are very happy that we were able to sign Claudio Pizarro, an internationally experienced and very prolific attacker," said sporting director Christian Nerlinger on the Bavarians' official website.
It marks a return to Bayern for Pizarro, who played for the club between 2001 and 2007, scoring 71 goals in 174 Bundesliga appearances, before departing for an indifferent spell with Chelsea.
However, he returned to Germany with Werder after only one season, another of his former clubs, and has successfully rebuilt his reputation as a prolific finisher on the continent.