The six-times European champions were twice ahead at the San Siro on Tuesday, but were hauled back on both occasions by Bayern defender Daniel van Buyten, the second time in the final minute of stoppage time.
The return leg will be played in Munich on April 11.
"The 2-2 draw leaves a bitter taste in the mouth, but to win in Munich all we need to do is play like we did in this match," defender Massimo Oddo was quoted as saying in Corriere dello Sport on Wednesday.
"We have to be pleased with our performance because our defence was excellent. Their goals were lucky goals, and we had a lot of bad luck. I think we'll make good in Munich and progress to the semi-finals."
Oddo's confidence was shared by his fellow defender Alessandro Nesta, who gave a solid performance despite only recently returning from injury.
"They aren't fabulous players, or at least they are not better than us," Nesta said.
"We were a bit shocked when we first got back to the dressing room, but we still believe we can go through."
Bayern's chances of winning the second leg look slim. The German side last beat Milan almost 20 years ago -- a 2-1 victory in the semi-finals of the 1989/90 European Cup.
Their two away goals, however, mean that a 0-0 or a 1-1 draw would be enough to put them through.
Bayern have already benefited from the away goals rule in this season's competition.
They drew 4-4 on aggregate with Real Madrid in the first knockout round and progressed at the Spanish team's expense thanks to two away goals at the Bernabeu.
The return from suspension of first-choice goalkeeper Oliver Kahn and midfielder Mark van Bommel will also strengthen the team.
The absence of Milan's leading scorer this season, Alberto Gilardino, who will be suspended after picking up a yellow card on Tuesday, leaves the tie delicately balanced.
Milan captain Paolo Maldini insisted there was no reason to believe his side could not reach their fourth Champions League semi-final in five years.
"It wasn't a positive result for us, but Bayern are beatable and I'd say we've got a 50-50 chance of progressing," he said.