Milito moved to 12 goals for the season with an inspired performance to cancel out an early goal from Andrea Montovani and a second-half hat-trick from Fabrizio Miccoli.
Milan, who remain one point behind leaders Juventus, whose match against Parma was postponed on Tuesday, were undone when Hernanes latched on to a loose ball to strike low into the net on 78 minutes.
Tommaso Rocchi then hammered home the decisive blow with a powerful finish from 10 metres five minutes from time as fourth placed Lazio moved to 39 points, four behind Milan.
Udinese, in third, beat Lecce 2-1 thanks to goals from Michele Pazienza and Antonio Di Natale while Thiago Ribeiro scored twice as Cagliari beat sixth placed Roma 4-2. Napoli drew 0-0 at home to Cesena.
Atalanta's clash with Genoa, Bologna's match against Fiorentina and Siena's game against Catania were all postponed due to bad weather.
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