Aston Villa had a couple of chances in extra time to get a point but Man U protected themselves and was noted for the tenth league match in a row without a loss.
Just before the hour was played, Villa equalized to 1-1.
After a short tussle with the defender, Bertrand Traore finally tucked the ball home.
Before the Villa players could barely cheer, Man United's Paul Pogba arranged a penalty that was videotaped, Pogba was hooked by Douglas Luiz and the replay pictures showed the light contact between the players' legs.
Bruno Fernandes put Man United ahead 2-1 hard down to the left from the penalty spot.
Sir Alex was present at the minute of silence
At the end of the first half, Marcus Rashford passed to Aaron Wan-Bissaka who from the right wing found Anthony Martial who threw himself forward and nodded in 1-0 between two Villa defenders and past Emiliano Martinez in the goal.
The match was preceded by a minute of silence for Tommy "The Doc" Docherty, who died yesterday at the age of 92.
He coached Manchester United between 1972 and 1977. The legendary coach Sir Alex Ferguson, 79, was one of those who followed the ceremony on site at Old Trafford wearing a black muzzle with the club's emblem.