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The 33-year-old bid farewell to Bayern last month after eight years at the club, and his contract officially expires on June 30.
On Monday, both Flamengo and Bayern confirmed that the full-back had signed a two-year deal at the five-time Brazilian champions, ending a 14-year spell in European football.
Rafinha joined Bayern from Genoa in 2011, having previously spent five years at Bundesliga rivals Schalke.
With 266 appearances and 18 titles in his eight years at Bayern, he played a role in one of the most successful decades in the club's history.
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Though never a first-team regular, the Brazilian was a highly popular figure in the dressing room, and was given an emotional send-off alongside Arjen Robben and Franck Ribery in May.