The goals of the 24-year-old saw him the 25-year record of Cristiano Lucarelli as the second player in the club's history to score at least twice against the San Siro Giants in a Serie A match.
In an exciting five-goal competition in stadio via del Mare, Krstovic placed the hosts in front in the seventh minute and found the bottom corner from the edge of the box with an assist by Johann Helgason.
He completed his brace in the 59th minute, but it was the visitors who came at the top, while Christian Pulisic yielded the winning goal.
The result ensured that AC Milan avoided a fourth consecutive Serie A defeat, a streak that they had not experienced since April 1986, after previous losses to Torino, Bologna and Lazio.