Brahim Diaz and Portuguese pair Rafael Leao and Diogo Dalot shared the goals for Milan, who extended their unbeaten run to 23 games in all competitions and top Group H with six points from two matches.
Diaz started and finished the move as he put Milan ahead in the 24th minute. The Spaniard dispossessed David Lischka, laid the ball off for Ibrahimovic, collected the return pass and fired into the net.
Lischka was in trouble again 12 minutes later, conceding a penalty with a foul on Ibrahimovic, but the 39-year-old Swede fired against the crossbar from the spot.
Ibrahimovic also missed a penalty against Cagliari on the final day of last season and again in the derby against Inter Milan, although he scored from the rebound.
It did not really matter as Leao turned the ball in from Dalot's cross in the 57th minute and Dalot scored the third from a raking Ismael Bennacer pass 10 minutes later.