The home side had given as good as they had got for long periods, but were undone by two clinical pieces of finishing by Deeney – a player signed for the Hornets by the current Wigan boss, Malky Mackay.
The opening goal came nine minutes into the second period, Deeney getting on the end of a nice cross from Adlene Guedioura to head powerfully past Ali Al Habsi.
Then, with 90 minutes played, Fernando Forestieri was felled in the penalty area by a despairing lunge from Emmerson Boyce, earning a spot-kick. Deeney sent Al Habsi the wrong way to secure the three points for the visitors.
Relegation-threatened Wigan never gave up the fight but remain winless on home soil for over six months heading into Saturday’s visit of local rivals Bolton.
It was a triumphant return to the DW Stadium for Ben Watson, Wigan’s FA Cup-winning goalscorer whose January move to Vicarage Road has ignited the Hornets’ promotion push.
Both sides went into the game urgently needing points for differing reasons, and it was the visitors who showed first.
Matej Vydra raced over half the length of the field towards the Wigan goal, and he looked ready to pull the trigger before Boyce appeared in the nick of time to clear.
Tommie Hoban’s cross then found the head of Deeney, but the striker’s header did not trouble Al Habsi.
After Wigan had a goal by Leon Clarke chalked off for offside, Deeney again worked Al Habsi with another goal-bound header.
Right on half-time, Marc-Antoine Fortune had Wigan’s best chance of the first 45 minutes, but his half-volley was straight at Heurelho Gomes.
Wigan picked up where they had left off after the break and squandered a great chance to nose in front.
Jermaine Pennant’s right-wing cross found Sheyi Ojo unmarked on the far post, but the teenager’s finish was way off target and the visitors had a let-off.
A quick free-kick from Wigan then found Fortune inside the box, but Guedioura produced a fabulous block.
Having stemmed the Wigan tide, Watford flexed their attacking muscles and took the lead.
Guedioura was the man who led a devastating counter-attack, and his cross was headed into the corner by Deeney.
Wigan tried to respond by throwing on new boy Josh Murphy and William Kvist for Pennant and Ojo, but still the visitors were winning the arm wrestle.
Guedioura and Vydra narrowly failed to hit the target from good positions, before the points were sealed in the last minute.
Forestieri was caught in the area by Boyce as he shaped to shoot, and Deeney made no mistake to the delight of the visiting fans behind the goal.