A late strike from substitute Cristian Battocchio ensured Watford denied Wigan at least a point at Vicarage Road.
Clear cut opportunities were at a premium, but Wigan can regard themselves unlucky to have a Nick Powell goal disallowed for offside and to be denied a penalty when Powell was brought down by Lloyd Doyley.
Watford will be relieved to take all three points and move up to fourth in the Championship table.
Owen Coyle decided to make two changes from the victory over Ipswich, with wide men McManaman and Beausejour replaced by McArthur and Gomez. Gianfranco Zola made two changes from the side which had thumped Barnsley 5-1 last weekend.
Watford started strongly and had the first good chance in the 10th minute when Lewis McGugan put Troy Deeney through the Latics defence and he pulled the ball back for Daniel Pudil, but his shot was saved by Scott Carson.
Latics looked to have taken the lead eight minutes later when Manuel Almunia could only push James McClean’s low cross from the left-back into centre of the penalty area and Nick Powell converted the rebound, but the goal was ruled out for what looked to be a very marginal offside decision.
Wigan were once again without strikers Grant Holt and Shaun Maloney and lone striker Marc Antoine Fortune lasted only 24 minutes before having to be replaced by Callum McManaman.
The first half ended goalless, but Wigan started the second half strongly and Almunia made a couple of excellent saves first from Powell and then McClean.
Wigan then looked to have won a penalty when Lloyd Doyley fouled Powell in the penalty area. But unfortunately referee Madley refused appeals for a spot kick.
Latics looked to be heading for a hard-earned point, until the 82nd minute when Watford substitute Battacchio fired home from the edge of the area after a Davide Faraoni shot had been blocked.
A draw would probably have been a fair result but all three points went to the Hornets.
After the game the Watford manager Zola admitted to Skysports about Nick Powell’s first half strike “it wasn’t offside” and Latics boss Owen Coyle was justifiably aggrieved that the referee did not award a penalty when Powell had been fouled by Lloyd Doyley in the 18-yard box.
“There’s no debate,” Coyle said. “James McClean’s a yard-and-a-half onside. We knew at the time. Bizarre doesn’t cover it”.