McTominay headed home after just five minutes thanks to a perfectly placed corner-kick from Alex Telles. The Scotsman was given the captain's armband as Harry Maguire was rested, until Ole Gunnar Solskjaer was forced to bring Maguire on due to an Eric Bailly injury.
As for the Hornets, there was sadly no magic left for them in the FA Cup and they were knocked out despite a valiant effort.
With a run of tough fixtures to come for United, it was imperative for Solskjaer's side to get a win under their belt after their defeat to City earlier in the week.
Story of the game
United started with enthusiasm and intent, a typically fantastic corner from Telles set up McTominay - the captain on the night - to head home the opener inside the five minute mark.
Watford had the next big opportunity of the match despite having little possession. Adam Mesina's flick-on shot was goal-bound as United failed to deal with a deep free-kick. Dean Henderson came off his line to make the save which redirected the ball towards the goal, fortunately for the keeper Axel Tuanzebe was there to clear.
The Hornets had another great opportunity when the ball pinged off multiple players in the box, the Watford players believed the ball may have struck Eric Bailly's hand and appealed for a penalty. VAR took a look and stuck with the on-field decision of no penalty.
Watford had a great period of play in the second half of the first-half as they launched plenty of testing balls into the box for the United defenders to deal with. At times, the United defence looked overwhelmed with the physical presence Watford provided in the box.
Henderson came rushing out of his six-yard-box from a cross and clattered Bailly in the motion of clearing the ball. Bailly who has done well to avoid any injuries of late was forced off due to the collision. Harry Maguire - who was expecting a well-deserved rest - came on as the half-time whistle blew.
At the break, United led 1-0.
Despite having the lead, United still lacked any end product when going forward. At times they looked disjointed and were all over the place in their attack.
There were very few chances in the second half but as the game developed, Watford had plenty of possession and looked the more likely to bag a goal and an equaliser.
Solskjaer brought on the reinforcements to try and bury the game with 20 minutes to play. Anthony Martial and Marcus Rashford came on but did very little. Rashford had an opportunity to bury the game but he telegraphed his shot which allowed a comfortable save from Daniel Bachmann.
Watford piled on the pressure at the end but were just missing that cutting edge to get the equaliser. United, held on and advanced to the fourth round of the cup competition.
Meaningful fixtures to come for United
United will now look ahead to Tuesday night where they travel to Turf Moor for a fixture that could send them three points clear at the top of the Premier League. It would be the first time United would be top of the league table at this stage of the season since Sir Alex Ferguson left the club. They then travel to Merseyside where they face the current Champions, Liverpool, which should be a real blockbuster.