A stunning volley from Stephan El Shaarawy gave AS Roma their third straight 1-0 win, this time at home to midtable Bologna in a father-versus-son encounter, in Saturday's other game.
Champions Juventus joined Napoli on 28 points while Milan, who spent more than 200 million euros ($232 million) in the transfer market in the summer to try and revive their fortunes, were left languishing in eighth with 16.
Briefly boosted by a 4-1 win at Chievo on Wednesday, Milan have five wins, five defeats and one draw from their 11 games. Napoli host lowly Sassuolo on Sunday (1400 GMT).
"The match was played on equal terms, the difference was made by Higuain who scored two outrageous goals," said Milan coach Vincenzo Montella, whose position is likely to be the subject of more speculation.
"We created as many chances as them, including a number inside the area, but Juventus played well."
Milan started well but quickly fell away and Juve's growing pressure paid off in the 23rd minute when Paulo Dybala slipped the ball through to Higuain who drilled his shot past Gianluigi Donnarumma.
It was the Argentine's 100th Serie A goal in 153 games for Juventus and Napoli, adding to the 107 goals he scored in La Liga for Real Madrid.
Zlatan Ibrahimovic is the only other player in the last 20 years to have score 100 goals or more in two of Europe's big five leagues.
Nikola Kalinic had two good chances to level for Milan, just failing to connect with Fabio Borini's low cross and seeing a close-range effort tipped on to the bar by Gianluigi Buffon.
Juve struck again in the 63rd minute with a superbly-worked goal as Kwadwo Asamoah surged through the Milan midfield and found Higuain with the help of a Dybala dummy. Higuain, in turn, slipped his marker and scored from 20 metres with a low shot which went in off the foot the post.
Roma, whose coach Eusebio Di Francesco is the father of Bologna winger Federico, are fifth with 24 points from 10 games -- eight wins and two defeats -- despite resting several players ahead of Tuesday's Champions League match at home to Chelsea.
El Shaarawy settled the match in the 33rd minute, meeting Alessandro Florenzi's corner with a left-foot volley which flew in off the underside of the bar.
The goal came five minutes after Roma striker Edin Dzeko sent a free header wide from six metres. The Bosnian also had a goal disallowed for offside early in the second half.
Di Francesco nearly equalised for Bologna, just failing to make contact as he slid in to try and meet Emil Krafth's low cross.
(Writing by Brian Homewood in Basel, editing by Ed Osmond and Christian Radnedge)
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