Pogba, 25, has not enjoyed the best relationship with Mourinho since returning to the Red Devils but looks to be regaining his form once again.
The France international scored twice and registered an assist with his assured performance against the Swiss champions but paid special mention to the Portuguese tactician over his faith for penalty duties.
"I didn't have any doubts about taking the penalty," Pogba told MUTV. "I know I missed [against Burnley] -- Joe [Hart] got me that time.
"I have the confidence of the players to let me take it so I thank them for that and thanks the manager for letting me take it as well.
"The most important thing is to put the ball in and that's what happened and I'm happy."
The 2018 World Cup winner has now scored four goals and registered a single assist in six games across all competitions.