Milan took a deserved lead when Christian Pulisic scored in the 10th minute, after a run inside the penalty area, before Federico Dimarco equalised for Inter about 18 minutes later.
But defender Matteo Gabbia managed to evade his marker and headed into the top corner of the goal from a free kick in the 89th minute, scoring the last-gasp winner for Milan.
Inter goalkeeper Yann Sommer and Milan goalkeeper Mike Maignan successfully stopped many difficult shots throughout the match, until Gabbia was able to snatch the winning goal.
The win took some of the pressure off Milan coach Paulo Fonseca after a disappointing start to the season, with Milan claiming their first win in the city derby after six straight defeats to Inter.
Inter have 8 points, which puts them in sixth place, equal with Milan, which is one place behind them due to goal difference.
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