Chelsea still progressed to the knockout stages of the Champions League despite their loss to Basel, because of Schalke's draw with Steaua Bucharest, with the home side winning the game late on thanks to Mohamed Salah's fine finish.
And Mourinho admits qualifying is the only plus point his side can take from the match, in which they failed to have a single shot on target.
"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 to finish first, so that is the only positive thing."
Mourinho claimed he could see from the first minute his side were not right, and when asked what he did not like about the display he replied: "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."
Mourinho feels his players suffered from the fact that most of them went away on international duty and that all their energy upon their return went into their win over West Ham at the weekend.
"I think the team paid today the price for their international 15 days," he continued.
"The match against West Ham was crucial and everyone played a great intense game but I think today we paid a price, they were tired.
"There was no reaction, wrong decisions - so I am not so sad with them as I understand, the team was not fresh and maybe I should make more changes in the team.
"But when you get such a good performance against West Ham you have that temptation of playing the same team as they played so well, it is difficult to change them.
"I made one change with Eden (Hazard) as I thought he could make a difference coming from the bench but perhaps I should have changed more players.
"We should get a better result than this but I don't blame the players, we have to rest and prepare for the game at the weekend because even with the defeat because of the nine points we are through, and that is the minimum we could do and now we have to fight for the first position."
Samuel Eto'o was stretchered off in the first half with a groin problem, but Mourinho says they do not yet know the extent of his injury.
"We have to wait, he has an injury in the groin, but in this weather and hard pitches it is something that can happen," he added.
Sky Sports' Niall Quinn was less than impressed with the performance and says the big clubs don't fear Mourinho's men.
Quinn said: "It wasn't a great message to send out tonight and to be outfoxed by the manager Murat Yakin twice in this campaign will hurt Jose.
"I think there was a speed out of the traps from Basel which he probably expected but he'll be disappointed with the way his players handled it because it seemed to go on and on and they never really got hold of it.
"They knocked it around a bit better in the second-half but not enough to suggest that this was the performance of a big European powerhouse that was just having a bit of an off night and will come roaring back.
"There needs to be a little bit more happen for Chelsea for the big sides to fear them."