Holebas slammed the ball home in the early stages of the second half after Middlesbrough failed to clear but that was the only moment of real quality at the Riverside on Sunday afternoon.
The first half was largely forgettable with the decision making of referee Roger East the main talking point.
Antonio Barragan was awarded a harsh yellow card midway through the opening 45 minutes but escaped what should have been a second booking just 10 minutes later.
Neither side could muster a serious attempt on goal in the opening period, with a tame effort from Alvaro Negredo the closest either came before the break.
The deadlock was broken on 54 minutes when Isaac Success went to ground inside the area.
East ignored half-hearted penalty appeals from the Hornets but Boro failed to clear and the ball fell to Holebas.
The Greek full-back rifled the ball home from outside the box, leaving Victor Valdes rooted to the spot in the Middlesbrough goal, to score what would prove to be Watford's winner.
Boro's best chance to equalise came with about 20 minutes to go as a delightful cross from George Friend found Alvaro Negredo, but his headed effort was dealt with comfortably by Watford stopper Heurelho Gomes.
Success nearly doubled the visitors' advantage with 77 minutes on the clock after a great run towards goal but his shot was straight at Valdes.