City rivals Inter had moved ahead earlier with Lautaro Martinez scoring a hat-trick in a dominant 6-2 victory over lowly Crotone.
But Milan restored their one-point advantage thanks to a Franck Kessie penalty on 15 minutes after a foul on Ante Rebic with Rafael Leao grabbing an impressive second from a tight angle shortly after half-time.
Stefano Pioli's side held off the promoted southerners despite Sandro Tonali's sending off on 33 minutes after his yellow card was changed to red following a VAR review for a high tackle on Artur Ionita.
Gianluca Caprari missed a penalty after an hour for Benevento with Gianluigi Donnarumma decisive in goal as Milan stretched their unbeaten run to 27 games in the league going back to March.
"We're ambitious, we're not hiding it and we aim to win the next match as well against Juventus (on Wednesday)," warned Pioli.
Nine-time reigning champions Juventus, who are now seventh, are in action later Sunday against Udinese.