However, while Mourinho says that qualification is a "positive", he believes that Basel were worthy of their win and says he failed to enjoy a single moment of the match at St Jakob-Park.
"A bad performance, a deserved defeat. But because of other results, we qualify. That is the only positive thing from this night," he told BBC Sport.
"I did not like anything from the first minute. We started with a defensive mistake."
Despite that, the Chelsea boss feels that his players were unable to produce their best because of the international break and a "crucial" match against West Ham United, which Chelsea won 3-0.
He added: "The team only had a bit of stability and control in the second half. I felt the team was tired, they paid the price of the international break and a crucial match against West Ham.
"There was no reaction from the players, and wrong decisions. I am not sad with them, as I understand they were not fresh."
Chelsea's final match in Group E is at home to Steaua Bucharesti.