AC Milan striker Zlatan Ibrahimovic
Antonio Nocerino scored his sixth of the season to give Milan the lead and Zlatan Ibrahimovic doubled the tally from the spot.
Milan moved a point clear of Udinese and Juventus, which play on Sunday. Siena remains two points above the relegation zone after five defeats in six games.
In a dramatic finish in Florence, two late goals from German Denis and Andrea Masiello appeared to have given Atalanta victory over Fiorentina, but Stevan Jovetic leveled to secure a 2-2 draw.
Elsewhere, Chievo got back to winning ways as goals from Cyril Thereau and Gennaro Sardo secured a 2-0 victory over Cagliari.
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