Milan players were furious after the referee gave the home side a spot-kick when he judged Mattia De Sciglio to have handled.
Milan came within seconds of ending Juventus 17-month run of home league wins before a hugely controversial penalty gave the Serie A leader a 2-1 win in a stormy match Friday. Second-placed Roma have 59 points from 27 matches.
The Rossoneri's hopes of qualifying for the Europa League took a hit at the weekend following their loss to Juventus, coupled with a win for rivals Inter while Lazio could also build a gap with their result against Torino on Monday night.
Gab Marcotti examines the controversial penalty decision in stoppage time that saw Juventus past AC Milan.
Television pictures showed that Milan goalkeeper Gianluigi Donnarumma, who almost got a hand to Dybalas penalty, said "its not possible, its always them" to teammates as he left the field. They should try something else rather than always complain about referees.
However, Milan coach Vincenzo Montella managed to keep his cool and apologised for the angry reaction of his team.
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"If we stay this compact, for sure we will enter Europe", he added.
Deulofeu's searing pace on the left wing proved to be too much for the backtracking Juve defence and when he slipped in Bacca, the Colombian calmly poked home to score his fourth goal in three games. "I was already in the tunnel and I preferred not to see the penalty".
Dani Alves' left-footed flick went over the Milan defence and right into Benatia's path, who took a touch before blasting a volley from close range in the 30th minute.
The 18-year-old Milan goalkeeper produced a superb double save when he parried Sami Khedira's shot and then tipped Gonzalo Higuain's effort around the post from the rebound.
Milan had few chances in the second half, reduced to pot shots from distance and things started to unravel for them when Jose Sosa was sent off for a scything challenge on Kwadwo Asamoah in the 93rd minute.