The Spanish international was forced off in the 17th minute after picking up a hamstring problem. Mourinho, who had previously questioned the United medical team with regards to the situation, described it as a "bad injury".
"Ander is out, I don't know the final diagnosis but I know he is out for a few weeks. Whether it is two, three, four, five or six I don't know but it will be a few weeks - that is for sure."
The injury, which means that Paul Pogba will most likely be recalled into the first XI after being dropped on Wednesday, adds another player to Mourinho's list of absentees. With him on the sideline are: Phil Jones, Marouane Fellaini, Marcos Rojo, Daley Blind and Zlatan Ibrahimovic, who recently returned to training.
The 'Red Devils' will have to cope without these key players when they host Chelsea in Sunday's league clash, which could be vital in deciding who makes the top four.