Under former coach Jupp Heynckes, The Bavarians won the Bundesliga title, the German Cup and the Champions League last season to mirror the Treble achievement of Sir Alex Ferguson at Manchester United in 1999.
However, those trophies were won without Gomez as the regular first-choice striker on the team.
Now the 27-year-old is heading to Serie A in a bid to kick-start a career which lost its way due to injury and a lack of first-team starts, as Bayern chairman Karl-Heinz Rummenigge revealed on the club's official website (via Bleacher Report featured columnist Timothy Rapp).
It was Mario Gomez’s desire to leave Bayern and join Fiorentina. We've now accommodated his wishes.
He made a major contribution to two German championships and two DFB Cup triumphs. Naturally, the highlight was winning the Champions League victory and the treble last season.
I would like to thank him for all his efforts on behalf of FC Bayern. On behalf of FC Bayern, I'd like to wish him lots of luck and great success in Florence.
Guardiola has now taken over from Heynckes and is looking to the future with the German club, and the departure of Gomez is not a shock move with the former Barcelona coach linked to a number of strikers already this preseason.
Luis Suarez (via Colin Trott of The Sun) was one reported target while Borussia Dortmund coach Jurgen Klopp has told Welt Am Sonntag (via Miles Chambers of Goal.com) that Robert Lewandowski will join Bayern next summer.
The writing has been on the wall for Gomez for the past year, especially with the arrival of Mario Mandzukic from Wolfsburg last year.
The Croatian international scored 21 goals in 40 appearances for Bayern last season, capitalizing on the first-team opportunities as Gomez was sidelined for three months at the start of the season through injury.
Gomez still returned a haul of 19 goals in 32 games in all competitions for Heynckes' side during the 2012-13 campaign and admitted to the official Bayern website that he had mixed emotions about his departure.
Leaving the best club in the world was a tough personal decision.
Bayern Munich made it possible for me to achieve the greatest wish of any footballer: winning the Champions League. Moving on now is a huge step for me.
I love football, and just want to be playing more. My best wishes to FC Bayern. I’m absolutely convinced this team will remain just as successful as they already have been in the Champions League over the next three to four years.
The forward unfortunately got buried by the impressive depth of the Champions League victors. The tight competition for starting places at Bayern currently is indicative of a team riding high.
Gomez joined Bayern from Stuttgart in 2009 and went on to score 75 league goals in 115 appearances for the club during his time there.
Bayern's loss, though, is a major gain for Fiorentina. Gomez's transfer will cost an initial £13.7 million, and could rise to £17.2 million, according to Bild (via The Guardian).
The Viola finished fourth in the Serie A table last season, just two points behind third-placed AC Milan.
Gomez will join Fiorentina as another former Bayern forward Luca Toni departs for Verona.
Gomez's arrival at the Florence club is poised to set the wheels in motion for highly-touted striker Stevan Jovetic to make a move from Fiorentina to the Premier League, with Arsenal and Manchester City leading the chase after Juventus reportedly withdrew from the race, according to Charles Perrin of the Daily Express.