Spurs went two down inside 20 minutes, and Mourinho reacted by bringing Christian Eriksen on for Dier midway through the first half.
And Mourinho was quick to apologise to Dier, insisting his performance was not the reason for his substitution.
“The first thing I want to say is to publicly what I did in the dressing room is to apologise to Eric Dier. It is never easy for a player but not for the coaching staff either. It was for the team and we needed a different solution,” Mourinho told BT Sport.
“We were losing 2-0, they were closing really well and I needed a second man with Dele Alli to come into the pockets. It was between Dier and Harry Winks but a hard decision.
“They understand, Eric understands but the reality it is never a easy and to make it clear, it was about the team not individuals. I thought about taking out one of the centre-backs and putting Eric in defence.
“We have qualified for the next round, that is the important thing for all of us at the club and the fans. It was hard, they are a good team, very well organised and they attacked our self esteem and self confidence.
“I did not expert our boys to feel this pressure at home and they have not had the best results in the last few months. It was a tough time, more than the changes or the tactical talk, I told them to keep calm, keep confident and believe in ourselves.”
“The goal before half-time is important. I did not see it, I saw it later on the screen. When you are losing 2-0, if you are in control of the other result and you know a draw is enough to qualify then we can go for the draw in the second half and be pragmatic.
Mourinho also picked out a Spurs ballboy for praise as he played a major role, getting the ball back in play quickly, for Spurs’ second goal.
“I love intelligent ballboys like I was, and this kid today was brilliant. He read the game, understands the game and made an important assist, an important moment for him and he will never forget it.
“You need to defend better, press better which was the strategy of the game. I think some of the boys look tired to me, national team weeks are never easy, playing Saturday and then Tuesday and the pressure surrounding my first match.
“We had the data and the levels of intensity were really high against West Ham. today I decided to play with the same team and maybe I was wrong and should have made a couple of changes to give more energy.
“The boys gave everything, the feeling is good and we have difficult matches to come. We can look to the Bayern Munich game with different eyes.”