The Watford skipper's historic moment came in the 37th minute when he converted an Adlene Guedioura cross before the home side made the points safe midway through the second period with a stunning second from Odion Ighalo.
After both sides had spent the opening exchanges sparring with each other, Watford had the first chance when Deeney headed an Ikechi Anya cross wide.
Boro's first effort on goal was an ambitious one as Grant Leadbitter tried to catch Heurelho Gomes out with a powerfully-struck free-kick from all of 40 yards, but the Hornets goalkeeper was able to get across to save.
It was the home side who gradually began to look the more threatening as the first half progressed and they twice went close to taking the lead shortly after the 20-minute mark.
Dimi Konstantopoulous was forced into a good save with his legs at the foot of his near post to keep out an Anya shot after the Scotland international had been played in by Ighalo.
Soon after, Gabriele Angella got up well to connect with his side's first corner of the match from the right but his downward header went down and narrowly wide of the far post.
After Patrick Bamford had seen a shot deflected, Boro created their first clear opening when a George Friend cross picked out Lee Tomlin in space in the area but he sent a first-time effort straight at Gomes.
But history was made in the 37th minute when Jonathan Woodgate was unable to rise high enough to cut out an Guedioura cross from the right and Deeney took one touch before sliding the ball beneath Konstantopoulos to net his 20th of the season for the third campaign running.
An under-pressure Albert Adomah shot into the side netting as Boro looked to get back on terms after the restart, but it was their opponents that were soon beginning to ask the majority of the attacking questions.
Ighalo fired at Konstantopoulos after turning his man on the edge of the penalty area before Daniel Tozser and Ben Watson both saw well-struck efforts deflected behind.
But in the 65th minute Watford doubled their advantage with a stunning second goal.
The ball was played into Ighalo on the edge of the 18-yard box from the left and the striker took a couple of touches to turn away from Woodgate and onto his left foot before unleashing a wonderful shot that flew past Konstantopoulos and into the far corner.
Guedioura almost made it 3-0 in equally impressive fashion with a cushioned lob from the edge of the area that was dipping in until it was superbly tipped behind by the Boro keeper.
Source : PA
Source: PA