The coach feels his side were hindered by fitness issues in their home loss against the German side
Spurs went 1-0 down at home through Timo Werner’s penalty in the first leg of the last-16 tie.
The Premier League side were without star attackers Harry Kane and Son Heung-min, while Erik Lamela returned from injury to feature for the last 20 minutes.
And Mourinho feels his side did the best they could despite their fitness issues and believes they can recover in the second leg in Germany on March 10.
“Let’s be loyal to the boys and say that they did everything they could do,” he told Sky Sports after the game.
“Lamela, do you know how many training sessions he had with the team? Zero. Direct from injury, to recovering on the pitch with the physios to 20 minutes of a game in the Champions League.
“That is our team. You can look at it and see two perspectives. One perspective is of an amazing group with amazing guys that try everything, from another side you see how we are in this moment.
“You look at the other guys, they play with [Patrik] Schick, [Timo] Werner and [Christopher] Nkunku. Nkunku is tired, get out, on comes [Emil] Forsberg. Schick is tired, come off, there’s [Yussuf] Poulsen.
“This is our situation, it’s like going to a fight with a gun without bullets. So, we did what we could do, and I think if we scored before them the game would be different.
“You can tell me we had luck in some moments, but I disagree.
“What I’m worried about is not the 1-0, because that is an open result, we can go there and win the tie.
“What worries me is that these are our players for the next… I don’t know how many matches. We have to play in two days again.
“We could see Lucas absolutely dead, [Steven] Bergwijn absolutely dead, [Giovani] Lo Celso dead.
“We are really in trouble. If this was just for this game, I would say: ‘Okay no problem, 1-0, everything is open’. What worries me is that we have Premier League and FA Cup to play in too and that is our situation.
“I cannot be happier to have guys like them with the limitations we have.”
Spurs are in action again on Saturday when they travel to Stamford Bridge to take on London rivals Chelsea. And Mourinho expects Frank Lampard’s team to be in much better shape than his side when they meet in the early kick-off.
He added: “But here we go, and Chelsea drinking sparkling water with lemon and watching the game on TV. On Saturday morning, thank you very much for the choice, Saturday morning we are there again.”