Antonio Nocerino gave Milan a 14th-minute lead and Sulley Muntari appeared to head the second goal soon after, TV replays clearly showing the ball had gone over the line before goalkeeper Gianluigi Buffon clawed it away, but play was waved on.
Juve made the most of their escape and salvaged a point with seven minutes to go when substitute Alessandro Matri smashed in a right-foot volley from close range, just after he had a goal disallowed in another refereeing controversy.
"There's no sadness, we played a good match," Milan coach Massimiliano Allegri told the club's website. "The 'goal' would have damaged them and it would have been a different game."
Opposite number Antonio Conte told Sky Sports Italia: "I can say that two good goals were disallowed. I don't think Matri's counts for less."
Argentine striker Rodrigo Palacio scored twice in the last 18 minutes to give 10th-placed Genoa a 2-2 draw at home to Parma, who are 13th, in Saturday's other game.
The turning point came soon after when Philippe Mexes met Emanuelson's cross with a powerful header that Buffon parried straight to Muntari.
The Ghanaian's header clearly crossed the line before being pushed away by the goalkeeper but, while Milan's players celebrated, the referee waved play on amid general bewilderment.
"I'm going to be honest, we were let off in that situation but it went the other way in the second half. The game should have ended 2-2," Buffon told Juve's website.
Juve broke away immediately after the incident and nearly stole an equaliser when Marcelo Estigarribia's shot was turned away by Christian Abbiati.
Milan forward Robinho was in inspired form, showing the dribbling ability and trickery which earned him the nickname the 'King of the Stepovers' in his native Brazil, and forced Buffon to dive at his feet to prevent a second goal.
