Mourinho has been a constant critic of the fixture schedule this season, with runs in the FA Cup and Europa League adding to 38 Premier League games.
Speaking about Bailly after the match at Old Trafford, Mourinho told BT Sport: "I didn't see the incident, but he was phenomenal".
"I hope we can enjoy something similar after the final in Stockholm".
"I do not want to think about next season - I want to think about the final we have to play in". Because we work very hard. But if I was in your chair, maybe. We didn't choose Europa League - we had to do it!
"It's the only major trophy we have never won".
Paul Merson is confident Manchester United will beat Southampton at St Mary's in the Premier League on Wednesday night. We had a fantastic record of 25 matches.
Mourinho, who arrived last summer, has won the Community Shield and the EFL Cup and will lead his side in the Europa League final against Ajax next week as they look to seal Champions League qualification. How to develop a fabulous playing style which our fans like and which brings success.
The defeat against Tottenham means United are now likely to finish sixth.
He has also confirmed he will be handing a first-team debut to third-choice Joel Pereira, most likely in United's final league match of the season, against Crystal Palace.
United put in an underwhelming performance at White Hart Lane, but Mourinho was nonetheless pleased with what he saw.
Asked what his approach to selection would be, he said: "The same".
"We need three good goalkeepers and we have them, but only two are experienced", the Manchester United manager said. I don't know what is important for them. I don't think the board feels like that.
Because we don't fight, we know it's a big objective, we know that if we lose the final we don't play Champions League, we know that.
"But obviously, like we did against Arsenal, we didn't throw the match away".
'A final is a final and we have to go to the final with everything like Ajax does because they have finished the season and they do not any more football to play until the final.
He said: "We don't worry about pressure and opponents. And if we score three on Thursday, we could go through".
But Mourinho says that for the next two domestic matches it is more important to show a fighting spirit than to achieve a victory.