But, making his debut as United captain, Pogba lasted just 18 minutes of the Champions League Group A game before being forced off by an apparent left hamstring injury, with Fellaini taking his place.
The 24-year-old Frenchman reportedly left Old Trafford on crutches.
“I don’t know (what the severity is),” Mourinho told MUTV, the club’s in-house television station. “I just know from experience it’s a muscular injury. In my experience, muscular injury stops you from playing for a few weeks, I think.
“It looks for me too (like a hamstring injury) but I haven’t spoken yet to the medical department.”
But the United boss said he had midfield options for the weekend’s Premier League clash with Everton, including Ander Herrera, Michael Carrick, Fellaini and Nemanja Matic.
France will be hoping Pogba is fit in time to play in the crucial World Cup qualifier against Bulgaria on October 7.
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