The win was revenge for a 2-0 November defeat by bottom-of-the-table Watford as Boro took an important stride towards the 40-point safety mark.
Middlesbrough were full value for the points. Watford fought hard in the second half to try and pull the game round but a two-goal salvo inside four minutes crushed any hopes of saving a point.
Middlesbrough, who were heavily criticised for a sub-standard performance at West Ham last week, roared into the lead after only five minutes.
Adam Johnson put over a right-wing cross to the far post, where Stewart Downing headed the ball back for Viduka to accept an easy scoring chance from five yards.
Watford hit back to level the scores after 22 minutes through Damien Francis. From a Jordan Stewart free-kick Danny Shittu headed the ball into the path of Francis, who crashed a volley into the roof of the net.
Middlesbrough were soon back in the lead through skipper George Boateng. Johnson showed good skill out on the right before Boateng's shot struck team-mate Chris Riggott on the way into the net.
Watford introduced substitute Tamas Priskin, their leading scorer, for skipper Gavin Mahon at the start of the second half.
Watford had shown little penetration to date but Tommy Smith had a scoring chance from a right-wing cross by Steven Kabba.
Smith just failed to connect despite the hesitancy of central defender Robert Huth.
Viduka was then blatantly held back in the penalty area, but the referee ignored Middlesbrough's claims for a penalty.
Ben Foster, on loan from Manchester United, was a star performer in the Watford goal. Despite coming to the rescue on several occasions, Foster, however, had no chance with a two-goal burst in 75 and 79 minutes.
Viduka curled a brilliant shot into the far corner of the net and then laid on a goal for Fabio Rochemback.
Viduka earned a standing ovation when he was substituted in the final minutes.
Middlesbrough fans will desperately await the outcome of contract talks with the Australian international ace.
The contract of Viduka runs out in the summer and Middlesbrough will hope to hold on to his services. Boro, however, are certain to face tough competition for a player who has proved his worth in the Premiership in a 13-goal season.
Watford, to their credit, refused to throw in the towel, but fighting spirit and hard running will not keep them in the top-flight.