The southwest London club appeared limp following the weekend's 3-0 win at West Ham United, which came after most of the players were on international duty in the week leading up, and Mourinho believes that may have been the cause for their 1-0 loss at St Jakob-Park on Matchday 5 of the Champions League.
"I think the team paid today the price for their international 15 days," he told Sky Sports.
"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."
Despite the loss, Chelsea were able to book their spot in the Round of 16 thanks to Steaua Bucharest's scoreless draw with Schalke.
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