Harvey Elliott and Ben Brereton halved Watford's lead on two occasions but their efforts were not enough to see them end their four-game winless run.
• Story of the match
The game started with both sides showing some good attacking intent. Just two minutes in Joe Rothwell tested Daniel Bachmann from 12 yards out but his effort was easily collected by the Watford goalkeeper.
Munoz's men were very tidy with their build-up play in the early stages and looked to get down the sides of Blackburn through the lively Sarr and Sema.
Blackburn lacked real quality with their final ball and it meant that clear cut opportunities were of a premium to them and although the game was fairly even, Watford started creating the better of the chances.
Tom Cleverley struck a free-kick just over from 25 yards in the 17th minute and Sarr was put through by Will Hughes in the 23rd minute but his weak shot was well saved by Thomas Kaminski.
Watford's pressure then paid off just two minutes later when a long hopeful ball forward from Cleverley teased Kaminski in coming to clear his lines but the Hornets top scorer, Pedro, just got there first and expertly lobbed it over the onrushing goalkeeper.
The first-half really came to life after the first goal as Blackburn looked to try and get back into the game. In the 27th minute, Adam Armstrong went extremely close with a left-footed strike from outside of the box which just whistled past the top right corner.
Despite Blackburn's pressure, the away side then doubled their advantage in the 38th minute when on-loan Everton defender Jarrad Branthwaite failed to clear his lines. The ball found Pedro whose deflected shot was clawed away by Kaminski but only into the path of Sarr who made no mistake in tapping home the rebound.
Just as Watford looked like they might start running away with it, Blackburn found a way back into it two minutes before half time.
The ball bobbled around in the Watford penalty area, with Rothwell pouncing on a loose ball. He managed to find 17-year-old Harvey Elliott who had been unusually quiet and he beautifully powered the ball into the roof of the net with his right foot, giving Bachmann no chance.
After a lively first half, it was the Rovers who ended it the stronger of the two sides.
The second period started just as lively as the first. For the first ten or so minutes, it was extremely end to end. Blackburn got in some promising positions down the left flank with full-back Barry Douglas being the main instigator for the home side as a handful of shots and crosses were well blocked by Watford.
Munoz's men also had their fair share of chances. Sema had a shot after he was found all alone at the back post but Kaminski rushed out to close the angle and save.
Sarr then found space down the right as he capitalised on Douglas's high starting position but his ball that flashed across the face of goal just alluded Pedro.
In the 60th minute, Sema restored Watford's two-goal cushion. Blackburn were left short at the back and Pedro was allowed to find Sema on the right-wing; he shimmied past Ryan Nyambe and slotted home a low, hard-driven strike into the bottom right corner.
Blackburn looked to try and force their way back into the game but they continued to lack quality in the final third. Armstrong had an effort saved after a mistake from Cleverley and Elliott looked to create a number of openings.
The away side looked to have managed the game excellently but in the 81st-minute, substitute, Brereton halved their advantage. Stuart Downing whipped in a delightful corner and Brereton was there to throw himself at it and head powerfully past Bachmann.
Despite some late pressure from the Blue and Whites, they were unable to find an equaliser and they are now five games without a win.
Next up for Tony Mowbray's men is a trip to Coventry City as they look to find an important three points after five straight loses. Watford travel south to Bournemouth as they face another key game in their push for promotion.
• Stand out player
Ismaila Sarr - Watford
Sarr was Watford's main threat all evening and his pace was a big problem for Douglas at left-back for the Rovers.
The 22-year-old was alive enough to find the net for Watford's second goal when he pounced on a rebound. His quality in the final third was also excellent as he found teammates on a number of occasions with crosses or passes.
The Senegalese international completed seven crosses this evening had 44 touches and three shots on goal. His impact was key to Watford's victory.
• Takeaways from the game
Blackburn need to tighten up defensively
It was not all doom and gloom for Blackburn this evening as there was a handful of positives to take.
Going forward they constantly looked dangerous through the lively Elliott, Armstrong and Rothwell. The three are constantly looking to find each other and the understanding between caused Watford a number of problems.
The height and width that their full-backs - Nyambe and Douglas have is a huge positive and offers them a massive outlet when attacking.
What they need to do is ensure that when they do attack in numbers, they must recover. Too many occasions tonight, they were left short at the back and their lack of experience in their centre-halves is an issue when playing against top-quality forwards.
If they tighten up defensively, then they will begin to win games.
Watford can win in all kinds of ways
An important factor when pushing for promotion is winning in all types of ways. Watford were very good going forward this evening but they were by no means at their best.
Winning on the road when you are not at your best is a huge sign that a team is pushing for promotion.
Watford's ability to create chances and score goals put them into a position where they were comfortable but after a lapse in concentration defensively, they found themselves scrambling the three points over the line.
The key thing is that they still won. They didn't crumble and they managed to hold out. They are showing some real signs of a team capable of clutching automatic promotion.