Philippe Mexes and Mario Balotelli scored the goals at the Stadio Artemio Franchi as the Rossoneri celebrated a rare victory to reignite fading hope of qualifying for Europe next season.
La Viola's own European ambitions suffered a setback as they can practically write off clinching a place in the Champions League, with 10 points now separating them from third-placed Napoli.
Balotelli was brought back into the Milan starting XI by Seedorf, who had left him out in the 1-1 draw against Lazio at the weekend.
At the other end of the field, former Milan striker Alessandro Matri was the injured Mario Gomez's replacement, and he nearly marked his return to the starting XI with a goal, missing from close range in the eighth minute.
Balotelli wasted his first chance with a free-kick sailing into the Florence sky in the 21st minute before getting the opportunity to try again from almost the same position just a few minutes later.
This time, he managed to keep the ball down and test Neto, who could only parry the shot out to Mexes, who headed it into the unguarded goal.
Neto pushed a Sulley Muntari effort wide on the half-hour mark before doing the same to keep Adel Taarabt's shot out.
Muntari sent a volley over the crossbar as Milan looked to build on their lead before the break.
Fiorentina had two excellent chances to level matters early in the second half, but Matri again missed the target from close range before another Milan player, Massimo Ambrosini, shot into the side-netting.
Balotelli showed him how it should be done with his third free-kick of the evening finally finding the back of the net.
He curled his shot round the wall and into the top corner, beyond Neto's reach with 64 minutes on the clock.
Fiorentina could not find a way back into the game with Gonzalo Rodriguez and Juan Cuadrado both missing the target with Christian Abbiati spending a relatively quiet evening in the Milan goal.