The Blues were beaten by a late Mohamed Salah goal at St Jakob-Park to lose 1-0 but still managed to qualify for the knockout stages because of Steaua Bucharest's 0-0 draw with Schalke.
Mourinho was disappointed with the display of his charges but said he could at least take solace knowing they had reached the Round of 16.
"A bad performance, a deserved defeat - but because of other results we qualify mathematically and that is the only positive thing for this night that we qualify for last 16," Mourinho told Sky Sports.
"Now we have to get a result at home (against Steaua on December 11) to finish first, so that is the only positive thing."
When asked what was wrong with his side, Mourinho replied with: "Everything.
"I didn't like it from the first minute, we started with a defensive mistake immediately, the first time we were in the game we made a defensive mistake - I think we only had a little bit of stability and control in second-half but I felt the team was tired."
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