The rout was Juve's worst home loss in over 57 years as Mateo Retegui (penalty), Marten de Roon, Davide Zappacosta and Ademola Lookman all struck for the visitors.
Asked about apologising to the Juve support, Motta insisted: “I think we started a game that we knew was going to be complicated, against a team that wanted to make the most of our mistakes.
“After the penalty, without getting into the details of how debatable it was, that was a painful moment. We are a young team, we tried to pour forward and get back into the game, but that left gaps at the back.
“We struggled psychologically with that first goal and got unbalanced, giving Atalanta even more space to run into with players like Lookman and their wing-backs. After a defeat like this, we are sad, we are disappointed, but at the same time this talk of the Scudetto that you dragged us into will no longer be talked about.
“Now we have to regroup against another good side in Fiorentina and go forward.”
He added, “It is a defeat we do not like, but I do not put it on the same level as the defeat to Empoli (in the Coppa Italia). They are different situations. Our team started well and then after the penalty incident, the game changed.
“We needed to keep our balance and we didn’t do that, but it’s partly down to a lack of experience in the side.”
Despite the heavy defeat, Juve remain in fourth place on the Serie A table.