United's Sanchez likely to be out of action for a long time
The Chile forward has not had a scan to determine the full extent of the damage, but Mourinho described the problem as an "aggressive muscular injury" that left the 29-year-old screaming in pain.
"No scans yet. But the player is experienced, the player knows what the injury is," Mourinho told a news conference ahead of his team's trip to face Southampton in the Premier League on Saturday.
"Also, from the top of my experience, just the painful scream and the way the injury happened, I know it's going to be for a long time."
Mourinho said Sanchez's injury was more severe than the hamstring problem sustained by centre back Victor Lindelof against Crystal Palace on Saturday, which is expected to keep the Sweden international out of action until Christmas.
"It's not the little muscular injury that in one week or 10 days the player is ready, for me and also for Alexis, the feeling before the scans is that the grade is different than the (Victor) Lindelof one and the Lindelof one was not an easy one.
"I think Alexis has what I used to call an aggressive muscular injury... I don't want to risk by saying for how long he will be out but from my experience I would say he will not play this year."
Sanchez has struggled at United this season, scoring one goal in 12 appearances in all competitions so far.
He last started in their Champions League victory at Juventus on Nov. 7 and came off the bench in subsequent league games against Manchester City and Crystal Palace before being dropped from the squad for Tuesday's Champions League win over Young Boys.
United are seventh in the Premier League with 21 points from 13 games ahead of the trip to Southampton's St Mary's Stadium and Mourinho says his side need more consistency if they are to close the gap to the top four.
"We want to improve our position in the table, we want to close the gap to the top four, we want to be smelling these positions, if not there then just behind then just smelling for the second part of the season," he added. (Reporting by Simon Jennings in Bengaluru Editing by Toby Davis)
(With inputs from agencies.)