Fresh from scoring a hat-trick in the 5-0 win at Fulham in his previous outing, the Hornets captain gave his side the lead in the 20th minute, but Watford failed to build on that and were pegged back on the stroke of half-time by a Chris McCann header.
The Latics were a match for their opponents for much of the second half but they were undone with eight minutes remaining when Ikechi Anya claimed his second assist by sending over the cross for Deeney to head home the winner.
Both sides traded early shots but it was Scott Carson who was the busier of the two goalkeepers in the opening stages, going to ground to save a Gianni Munari shot before he was tested by a 30-yard free-kick from Daniel Tozser.
The Hornets had looked comfortable from the opening whistle and they were to take the lead in the 19th minute after Callum McManaman was booked for fouling Anya on the halfway line.
The free-kick was taken quickly and the ball was played up to Anya on the left side of the penalty area where he laid it in to Deeney, who slipped a low finish under Carson from the left side of the six-yard box.
Watford continued to move the ball around nicely at times after taking the lead, without creating too much of note, while their opponents never threatened until they won the first two corners of the match and Leon Barnett headed a McManaman free-kick tamely at Heurelho Gomes.
That offered the visitors encouragement though, and – combined with their opponents going off the boil in the latter stages of the first half – Gomes was forced to save a James McClean shot with his legs before the Latics equalised in the last minute of the opening period.
The Hornets failed to deal with a Roger Espinoza corner and McCann headed home to make it all square at the break.
And it was from another corner that Wigan went close to taking the lead seven minutes after the restart as Ben Watson flashed a near-post header narrowly over.
Wigan continued to look the better side for a spell, with McClean forcing Gomes to shovel his angled shot behind for a corner. Then, from the resultant corner, the Hornets keeper had to go to ground to deal with Watson’s inswinging delivery.
Watford slowly began to find their attacking feet again, although not with the same composure and confidence they had mustered in the opening 30 minutes.
But the moment of quality the home side had been craving arrived with eight minutes remaining.
Tozser set Anya away down the right and he got to the byline before hitting a deep cross which was too long for Munari but Deeney arrived at the far post to head home and make it 2-1.