After an even start to the match, Atalanta midfielder Malinovskyi broke the deadlock in the 29th minute with a powerful left-foot finish from the edge of the box.
Milan midfielder Bennacer scored the equaliser from a corner by Alexis Saelemaekers in the 68th minute, shooting through the Atalanta defenders and into the net off the post.
Milan dominated possession and had more attempts on goal but failed to make them count.
"I think we could have done better, we could have tried to win this match. It was difficult to find room, Atalanta were compact," Bennacer said after the match.
Atalanta were pleased with their performance.
"We played against the Italian champions and we need to be satisfied," midfielder Mario Pasalic said. "We start again from here and we have proven that we can play at this level against the strongest also this year."
Milan host Bologna on Saturday and Atalanta travel to Verona on Sunday.