The Argentine forward scored in either half to help the defending champions to the top of the table, with Milan languishing in eighth after a fourth defeat in six matches.
AC Milan started brightly in front of their own supporters with Ricardo Rodriguez forcing an early save out of Gianluigi Buffon, while Hakan Calhanoglu was proving a handful for the Juventus backline.
However, slowly but surely, the visitors found their rhythm and although Paulo Dybala failed to net with a speculative effort from distance, it was not long before Juventus went in front.
Dybala turned provider to set up strike partner Higuain, who drilled a venomous effort past Gianluigi Donnarumma from the edge of the area.
The goal rocked Milan but to their credit, they continued to threaten inside the final third, although only a weak Suso effort forced Buffon into any work.
Just before the break, the home side should have found their equaliser through Nikola Kalinic, but the Croatian's close-range effort struck the crossbar and bounced clear.
Chances were few and far between after the restart, with only a volley from Dybala threatening the goal, but on 63 minutes, Juventus were able to double their advantage.
After receiving a pass on the edge of the penalty area, Higuain did the rest with a brilliant effort which struck the post before finding the corner from 20 yards.
Rather than Milan mounting a comeback, it was Juve who looked more likely to score a third, with Giorgio Chiellini directing a header over the crossbar from a free kick.
Dybala - who had been a constant threat to the Milan defence - fizzed an effort from distance but it went straight at Donnarumma.
There was little action during the closing stages of the match with Juve doing an effective job in nullifying any threat offered by the home side, and Massimiliano Allegri will now start to feel that the top team in Italy are fully over their slow start to the campaign.