La Dea were behind straight from kick-off when Davide Calabria broke clear to score, whilst a Remo Freuler mistake allowed Sandro Tonali to double the lead.
Milan went further ahead late on as Rafael Leao finished off a quick counterattack, but La Dea threatened a comeback when Duvan Zapata drilled in a penalty, before he set up Mario Pasalic to tap in a second in stoppage time.
Musso 5.5; Djimsiti 6, Demiral 6.5 (’46 Koopmeiners 6), Palomino 5.5; Zappacosta 5.5, De Roon 6, Freuler 5 (’87 Pasalic 6.5), Maehle 5.5 (’56 Muriel 6.5); Pessina 6 (’24 Pezzella 5.5); Malinovskyi 6 (’56 Ilicic 6), Zapata 7
Player of the match: Duvan Zapata
A rare bright spot in an otherwise hugely disappointing display from Atalanta, although the Colombian was far from his best. He blasted his penalty beyond Maignan to give hope of a comeback, before teeing up Pasalic with a good cross to make the final moments more tense.