Speaking at a press conference, the 33-year-old admitted that his time with the Bavarians was coming to an end when his contract expires in June.
He joins wing duo Arjen Robben and Franck Ribery in bidding farewell to the Allianz Arena as Bayern begin a period of rebuilding.
He has helped the club win six successive Bundesliga championships as well as contributing to three DFB-Pokal successes and the Champions League title in 2013 as Jupp Heynckes' side claimed the treble.
"The eight years have been wonderful, I've had some great moments here," he said as his departure was announced. "The treble in 2013 was special. All things come to an end eventually.
"We are together every day and know each other so well - we are a family. The friendship we all have is the greatest thing."
Rafinha will hope he can help contribute to winning two further trophies in his final weeks with the club as Niko Kovac looks to end a difficult first campaign in charge with victories in both the Bundesliga and the Pokal.
A win over Eintracht Frankfurt on the final day of the league season will secure a seventh straight domestic title, though a defeat could allow long-time leaders Borussia Dortmund to claw back to the summit with a win of their own over Borussia Monchengladbach.
Bayern then face RB Leipzig on May 25 in the Pokal final, with Kovac looking to defend the trophy he won with Eintracht last season.
Rafinha's final season with the club has been marred by disputes with Kovac over his lack of playing time.
The former Schalke defender has made just 26 appearances in all competitions, and spoke out in February against what he deemed unfair treatment from his Croatian coach.
"I do my work and train well, but the coach does not count on me," he told reporters ahead of Bayern's Champions League meeting with Liverpool.
"I do not know why. I have not made any problems. But of course I am disappointed."
Rafinha's next club is yet to be confirmed, though he has been linked with a return to his homeland with Flamengo.