The 27-year-old, released by the Villans as a youngster, turned the game on its head after the visitors twice held the lead in Hertfordshire.
Villa were on the brink of just a fourth league win of the season when Jordan Ayew restored his side's advantage early in the second half, but a red card shown to Aly Cissokho would prove to be a big turning point.
Watford switched from their intricate style that had failed for much of the game to a more direct approach, and it paid off in some style with two goals from Birmingham-born Deeney in added time to secure all three points.
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Befitting the end-of-season feel to the match, the opening quarter of the contest saw chances kept to a premium with neither side able to find a single shot on target.
That made way for a far more exciting 20-minute spell leading up to the interval, however, beginning with a fine Ben Watson attempt which crashed back off the Villa upright.
The midfielder teed himself up for a 25-yard volley, which had the beating of the returning Mark Bunn but just lacked the dip to find its way under the crossbar to open the scoring.
Three minutes later the visitors were ahead, thanks to Ciaran Clark's first goal of the campaign that came via a simple set-piece delivery into a central position.
Clark simply slipped past marker Craig Cathcart and nodded the ball down the middle to give the Villans a rare lead, which they so very nearly added to later in the half.
Cissokho crossed from the left and did well to pick out Ayew, whose subsequent header came back off the post and was eventually cleared to safety.
Almen Abdi dispatched the resultant free kick, bending the ball up and over the wall and out of Bunn's reach to level things up with the final meaningful act of the half.
Villa were quick to regain their lead following the restart, however, when a nice piece of link-up play between Rudy Gestede and Ayew ended with the latter rifling into the corner from the edge of the box.
There was more intricate build-up play to follow, too, as Ayew this time slipped in Gestede just two minutes later for the striker to blast well over the bar, signalling a few boos from the home end.
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Watford, with three wins in their last 11 in all competitions now, nearly swung momentum back their way just before the hour only for match-winner Deeney's header to be cleared off the line by Cathcart.
Despite being the division's lowest scorers it was Villa who were proving to be the more threatening in attack, and they perhaps should have had a third when teenage full debutant Kevin Toner guided his free header wide of the far post.
More attempts were to follow at either end in the final quarter of the match; substitute Steven Berghuis seeing his deflected shot easily collected by Bunn before Gestede's side-footed effort was blocked aside by Cathcart.
Villa were looking comfortable enough as the match wore on, but they were reduced to 10 men with 15 minutes still left to play when last man Cissokho brought down Anya.
A simple punt up field from Watson allowed the Scotland international to burst into acres of space, with referee Anthony Taylor left with little choice after Cissokho lunged in.
Despite seeing their opponents being reduced to 10 men it looked like being an afternoon to forget for the Londoners, until Deeney converted Berghuis's cross from the right in the 90th minute, before smashing home a loose ball two minutes later to win the game.