Despite the hosts shading possession and chances throughout the game, neither side looked to be totally on top at any stage and the match was decided by Jose Holebas' second-half stunner.
The Greek left-wing back scored with a searing shot into the top corner from the edge of the penalty area early in the second half to see Watford move up in the table and leave Middlesbrough looking over their shoulders at the bottom three.
Hosts edge goalless first half
Both managers made two changes from their sides' previous games. Alvaro Negredo and Gaston Ramirez returned in attack for the hosts, while Miguel Britos came in for Watford alongside Isaac Success, who was handed his first start for the club.
The opening half an hour to the game was largely a quiet one, with no real clear-cut chances for either sides. Boro shaded the half with more possession and the only opportunities, but a nil-nil scoreline at half-time was a good representation of the play.
Stewart Downing fired a shot wide from close range after a penalty shout was closed down while Gaston Ramirez pulled a left-footed effort across the goal after a burst through the centre, while Watford's attacks largely broke down in wide positions following fouls or blocked crosses.
Antonio Barragan was perhaps lucky to remain on the pitch as long as he did after a number of fouls on the dynamic Isaac Success, and he was withdrawn in the second half with a red card surely looming.
Holebas magic settles game
The only goal of the game came out of nowhere, and indeed it was the Hornets' first shot on target in the game.
Ten minutes into the second half, a Watford penalty shout was waved away as Success went down under the challenge of Adam Forshaw, but the ball was cleared only as far as Holebas, who fired a screaming shot into the top left corner from the edge of the penalty area.
What had been a tense game opened up as Boro pressed forward and Watford looked to counter, but niggling fouls and constant time-wasting meant that the match lacked any sort of rhythm and neither side managed to build up a head of steam.
Middlesbrough were improved by the introduction of Barcelona youth product Adama Traore, with his direct style and pace a marked upgrade on the ineffective presence of Cristhian Stuani on the right.
Watford on the up as bottom three looms for Boro
However, despite half an hour of huffing and puffing in both directions, neither side truly threatened to add a second goal to the game.
Six minutes of stoppage time passed by largely without incident and the frustration among the home fans was evident on the final whistle. With six points from eight games and an immensely difficult run of fixtures ahead, Aitor Karanka's side are now without doubt entrenched in the relegation dogfight.
For Walter Mazzarri, his side moved up to ninth in the fledgling league table with eleven points from their eight games - though a win for Southampton against Burnley on Sunday afternoon would see them back down to tenth.