The Red Devils moved to within five points of leaders Manchester City courtesy of a 4-2 win at Vicarage Road but they had been cruising at the break.
Former Watford winger Ashley Young scored two stunning goals inside six minutes to break a scoring duck stretching back to May 2016 and, when Anthony Martial tucked home a third, the visitors looked home and hosed.
Instead, Watford hit back as substitute Troy Deeney converted a 77th-minute penalty before Abdoulaye Doucoure turned home to bring Marco Silva's side within one goal.
The points would be secured in style as Jesse Lingard scored a fantastic solo effort after running at the Watford defence.
Lindelof, 23, has started United's last three Premier League games following a slow start to life at Old Trafford following his big-money move from Benfica in the summer.
He was named man of the match in the 1-0 win over Brighton last weekend and did well to keep the likes of Andre Gray and Richarlison at bay for much of Tuesday's contest.
"I think Richarlison is a very good player and a difficult player to play against but Victor is very fast," Mourinho told MUTV.
"He has adapted to play centrally but also to go to the sides because he's got the agility that many of the central defenders don't have.
"I think it was another very positive performance by Victor."
Like Lindelof, Martial has established himself in the United side in recent weeks having been in and out of the team as he rotated with Marcus Rashford.
Mourinho was equally pleased with the France international's contribution at Watford - even if he believes there is still more to come from the former Monaco man.
"I am pleased," he said of Martial's performance.
"I think he suffers a little bit with accumulation of matches
I could feel that in the second half he was going down and down and down.
"He's still a young guy and his body, his biological situation has space to improve but in the first half, during the time, he had strength and explosion in his legs
He was dangerous and scored an important goal."
Doucoure, whose strike gave Watford hope of salvaging a famous point before Lingard's effort kept them at bay, admits lessons must be learnt ahead of Saturday's visit of Tottenham.
"To learn in these situations you have to take the positives," he told watfordfc.com.
"We came back to 3-2 so it is good for the team and we come back against Tottenham and Saturday and play the same as we did in the second half and we can achieve some objectives.
"I think Spurs will come here like Man United, they are a very strong team with big players so we have to concede less goals to get a result against this type of team and of course we can do that on Saturday.
"You concede three goals in the first half against this kind of team and it is very hard to come back after."
Source : PA