Mourinho's men had had spells of dominance in the game, but were by no means in charge of the game as it headed towards half time.
Ashley Young was the provider of the first, as he swung a ball in from the left that took a refelction on the way. Watford appealed for offside against Romelu Lukaku, but the flag didn't go up and he bundled the ball in to the net.
Within just four minutes, the second goal came from a corner from the right.
The height of Belgian midfielder Marouane Fellaini was put to good use as he headed the ball to Chris Smalling, who controlled the ball on his chest and unleashed a fierce volley on his weaker foot high in to the net.
Smalling's effort caused an eruption of celebration from Jose Mourinho, as his team looked to be in the driving seat just before the break.