Borowski returns to Bremen
The 29-year-old, whose contract with Bayern ran until 2011, failed to win a starting place at Bayern last season.
"I had a curious year at Bayern but would not want to miss out on this great experience," Borowski told reporters.
Borowski, who played from 2001 to 2008 for Werder, will sign a three-year deal with an option for one more, the club said.
German media reported the transfer fee was about five million euros.