United entered the match knowing that a point would be enough to book their spot in the last-16 stage of the Champions League, but the Red Devils conceded in the 89th minute as they were made to wait to secure qualification.
Pogba was replaced in the second half as Mourinho continues to protect the Frenchman, but the United boss has admitted that the midfielder's exit played a role in the English giants losing the match.
"Did Pogba coming off have an impact on the team? I think it did have an impact, we were not such a good team after Paul came off but it had to be with the levels of fatigue after 65 minutes," Mourinho told reporters.
"I brought to the pitch an experienced player like [Nemanja] Matic and thought it couldn't affect the game. I bring Marcus [Rashford] to give us more speed, more problems to them, Zlatan [Ibrahimovic] to hold the ball and the approach was good."
United will look to bounce back from the defeat when they welcome Brighton & Hove Albion to Old Trafford in the Premier League on Saturday afternoon.