The organisation's disciplinary committee will assess video footage of the match, which left defending champions Milan a point clear of Juve at the Serie A summit, having played a game more.
Milan's French centre-back Mexes punched former Roma colleague Marco Borriello in the side early in the second half, while his Ghanaian team-mate Muntari is accused of violently shoving Stephan Lichtsteiner.
Milan old boy Pirlo, meanwhile, is accused of elbowing Mark van Bommel.
Juve finished the match at San Siro with 10 men after Chilean midfielder Arturo Vidal was shown a late red card for a challenge from behind on Dutch enforcer van Bommel.
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