Having overcome a back problem to start, Higuain - moved out on loan following Cristiano Ronaldo's arrival in Turin - might have wished he skipped the visit of his parent club after Wojciech Szczesny denied him from the spot in the 41st minute.
The champions had already established an eighth-minute lead through Mario Mandzukic and made the result safe thanks to Ronaldo's sealer nine minutes from time.
Their clean sheet, and with it a six-point lead at the top, came despite Leonardo Bonucci watching from the bench at the ground where he spent a mixed 12 months.
Milan's confidence from a three-match Serie A winning streak was quickly eroded as Mandzukic climbed above Ricardo Rodriguez and met Alex Sandro's cross with a commanding downward header.
100 - Mario Mandzukic has scored the 100th Juventus’ Serie A goal in away games against Milan. Milestone. #MilanJuve— OptaPaolo (@OptaPaolo) November 11, 2018
Their misery deepened just before the break with Higuain, who won the penalty via a VAR review of Medhi Benatia's handball, out-thought from the spot.
Szczesny instructed his former team-mate to shoot to the left and Higuain obliged, allowing the goalkeeper to make his second penalty save against the Rossoneri.
Ronaldo, quiet in the first half, forced Gianluigi Donnarumma into a smart stop soon after the restart, before his goal arrived from a kind rebound in the 81st minute.
And, after receiving a receiving a talking to from the referee, Higuain ranted his way into an early bath to cap a miserable night for himself and Milan.
What does it mean? Break good for Bianconeri
They won comfortably in the end and were rarely troubled defensively, but Massimiliano Allegri will still welcome the international break as a chance to take stock after a performance that was not exactly fluent.
Szczesny stands up at San Siro
Higuain took a risk when he opted to take on a man who must have faced him from the spot many times over in training. The decision backfired: Szczesny called on all of his insider knowledge to foil the forward for the game's decisive moment.
Higuain drops Milan in a hole
It was clearly a frustrating outing for Higuain and yet his late meltdown leaves Gennaro Gattuso with greater ramifications than were necessary from this defeat. The Rossoneri boss is now required to mull over his attacking options.
Key Opta Facts
- Juve's tally of 34 points from the first 12 league games is a record in Serie A history.
- Juve have won 13 away league games in 2018, more than any other team in the top five European leagues.
- Gonzalo Higuain has missed his last two penalties in Serie A after having scored four in a row.
- Juventus have won 11 of the last 12 league games against Milan (L1).