In what was Ole Gunnar Solskjaer's first match since being appointed permanent boss, the Red Devils secured three important points to return to the Champions League positions.
United's team showed four changes from the one that started the FA Cup defeat at Wolverhampton Wanderers before the international break. Phil Jones, Ashley Young, Juan Mata and David de Gea all came in, with Sergio Romero, Jesse Lingard, Victor Lindelof and Diogo Dalot dropping out.
Doucoure had the game's first half-chance in the sixth minute, but the midfielder fired wide of the post from inside the United box, before Deeney missed the target from distance two minutes later.
Chris Smalling then headed wide of the Watford goal in the 10th minute as the home side had their first opportunity, but Javi Gracia's side remained on top and De Gea had to claw away a header from Deeney shortly after.
De Gea was then again called into action down the other end, having to fly across his goal to keep out a powerful strike from Pereyra with Watford continuing to find space in dangerous positions.
Deulofeu was next to bring a save from De Gea in the 25th minute, before Martial had a penalty shout turned down after going down inside the box under a challenge from Miguel Britos.
United did make the breakthrough in the 28th minute, though, when Rashford raced onto an excellent pass from Luke Shaw before lifting the ball over the onrushing Foster.
Only a smart save from the Watford goalkeeper prevented Martial from smashing the home side two goals ahead in the 33rd minute, meanwhile, with the away side failing to deal with a corner.
Rashford's pace continued to cause the capital outfit issues in the latter stages of the first half, but United will have felt fortunate to have entered the half-time break ahead, with Watford having more opportunities in the opening 45 minutes of action.
Deulofeu tested De Gea from distance in the early stages of the second period, before Daryl Janmaat missed the target from inside the United box as the visitors continued to threaten.
De Gea made some excellent stops on the afternoon, but one of his best arrived in the 53rd minute when he got down low to turn a Pereyra effort past the post.
There was not too much for the United fans to get excited about down the other end, though, with Solskjaer's team struggling to get going in the first 15 minutes of the second half.
Watford had another opportunity when Will Hughes found space inside the home side's box, but the midfielder's effort just curled wide of the far post as United stayed ahead.
United found a second in the 72nd minute, however, when Martial managed to scoop the ball home from close range having initially seen his effort saved by Foster, with the goalkeeper unable to react to the second strike.
Watford threatened to make it an uncomfortable finish when Doucoure converted for 2-1 in the 90th minute, but United held on to secure an three important points in their battle to finish in the top four.
Next up for United is a trip to Wolverhampton Wanderers on Tuesday, while Watford will attempt to return to winning ways when they host struggling Fulham on the same night.
MANCHESTER UNITED (4-3-3): De Gea; Young, Jones, Smalling, Shaw; Herrera (Pereira 63'), Matic, Pogba; Mata (Lingard 63'), Rashford, Martial (Rojo 77')
WATFORD (4-4-2): Foster; Janmaat (Kiko 56'), Kabasele, Britos, Masina; Hughes (Success 82'), Doucoure, Capoue, Pereyra; Deeney, Deulofeu (Gray 74') body check tags ::