"We played very well in the first half, opened the scoring and had the chances to extend our advantage. It was very negative to go into the break with a 1-1 scoreline, we deserved more," said coach Carlo Ancelotti.
"In the second half we tried to get back in front, but a defensive error allowed Atalanta to score their second goal and then close up all the spaces, so it became far more difficult.
Kakha Kaladze was caught out for the Atalanta winner scored by Nando Tissone.
"It was a mistake, the pitch was slippery and this can happen. It was a mistake that cost us dearly, though."
Atalanta did not expect this victory and it was a special one for the team that hopes President Ruggeri will emerge from his coma following an aneurysm.
"This win was for the President," said goalscorer Tissone. "He was our first thought. We did everything away to Genoa looking for victory and couldn't do it, but now we have."
Coach Luigi Del Neri also dedicated the result to Ruggeri. "He is a man with the courage of his convictions and we all respect him. We will try to give him strength any way we can. I hope when he returns to us, someone will tell him what the team achieved and this can raise his spirits.
"As for the match, if you give Milan space, they will hurt you, so we faced them in the perfect way. We never gave the impression we were under pressure."