The midfielder curled in the game's opener before Borja Valero doubled the lead, and Giampaolo Pazzini's strike was rendered meaningless by Mounir El Hamdaoui's late cracker
Alberto Aquilani stroked in the opening goal on his return to San Siro, the ground which the Italian midfielder had spent last season on loan from Liverpool.
Borja Valero extended the Viola lead seven minutes from half-time a few minutes after Alexandre Pato spectacularly skied a penalty over the crossbar.
Substitute Giampaolo Pazzini restored hope among the home fans with a tap-in after Philippe Mexes' skilful shot rebounded off the post, but Mounir El Hamdaoui's beautiful finish with less than three minutes left ensured they collected all three points.
Napoli’s win over Genoa on Sunday means the Florence-based club stay fourth in the table, while Milan are guaranteed to end the weekend outside of the top 10 with their fourth San Siro defeat in seven league matches this season.
The Rossoneri began the game at a crawl, Facundo Roncaglia’s powerful, 25-yard pot shot and Juan Cuadrado’s surging runs meant the home atmosphere became subdued quickly. Stephan El Shaarawy was looking energetic at the other end and cannoned a couple of shots just off-target, but nothing concrete came of any early forays forward.
Fiorentina grabbed the game by the scruff of the neck with 10 minutes gone, though, Adem Ljajic teeing up Aquilani 12 yards from goal, allowing the midfielder curl it past an outstretched Christian Abbiati with his first touch.
The next 15 minutes were characterised by a sparsely-filled San Siro groaning in unison as Rossoneri players continuously failed to time their runs with precision and were regularly called offside.
An opportunity for Milan to equalise presented itself after Roncaglia was yellow carded for clattering into Pato inside the 18-yard box on 33 minutes, but the Brazilian attacker missed the penalty, sending his effort high over the crossbar in embarrassing fashion.
Valero capitalised on the distracted Milan side, burrowing a hole through their defence from the left edge of the box, wiggling past a flailing Mexes and striking low into the far corner of the net.
The second half started with Milan in the ascendancy, with Bojan Krkic and Pazzini brought on the freshen the attack up. Kevin-Prince Boateng headed millimetres wide of the left post from six yards out in the best chance to score for either side within 10 minutes of play recommencing.
It was Pazzini who pulled a goal back for the home side, pouncing on a loose ball five yards from goal after Mexes hit the post from 15 yards with an outrageous backheel.
The goal upped the game’s tempo significantly, as the visitors pressed to extend their lead while the hosts fought to score an equaliser, causing an extraordinarily open encounter.
San Siro season ticket holders might have expected an equaliser, but it was Fiorentina who had the better chances as the game came to a close. Mattia hit the post in the last five minutes before El Hamdaoui chipped over Abbiati from 25 yards to emphatically end the contest in the Viola’s favour.