It was all going so well for Villa, who took the lead twice in the game, only for Birmingham City fan Deeney to score twice at the death, after the visitors had been reduced to 10 men following Aly Cissokho's red card.
The managerless side have now lost a club record 11 Premier League games in a row, another disappointing day as the already relegated team await the end of the season.
Bright start from an improved Villa team
Lining up in a 5-3-2 formation with Kevin Toner given a first team debut at centre-back, Villa started Rudy Gestede and Jordan Ayew together up-front, a partnership that fans feel could have been used more often this season.
They sat fairly deep to begin with, fairly unsurprising given the defensive formation, inviting Watford pressure. The Hornets struggled to get through the back of Villa's defence, but did hit the woodwork as a Ben Watson strike from distance rattled off the bar.
That was a lucky escape, one that they capitalised on a few minutes later, Ciaran Clark scoring the opener. The defender rose highest from Ashley Westwood's corner, heading down and into the net.
Ayew nearly doubled the lead around 15 minutes later, Idrissa Gueye finding him with a cross, the striker's header coming back off the post.
Two quick goals
Villa too, would be made to pay after hitting the woodwork, as Watford grabbed an equaliser just short of half-time. Another set-piece, Villa's wall didn't cover themselves in glory as Almen Abdi looped the ball into the corner of the net from a free-kick.
They certainly didn't let it get them down though, coming straight out of the traps after the interval, Ayew making it 1-2. Good passing through the midfield culminated in Gestede and Ayew playing a one-two on the edge of the box, before the latter sent the ball into the corner for his seventh goal of the season.
Cissokho red card the catalyst for capitulation
It was going well for the away side, who could have made it 3-1 minutes after Ayew's goal as the striker set up Gestede who missed a good chance, but it was almost going too well given their season - and it was.
Aly Cissokho brought down Ikechi Anya as the Hornet was racing through on goal, leaving referee Anthony Taylor with no choice other than to reduce the Villans to 10 men.
From then on, Watford went for the throat, Deeney eventually taking advantage in stoppage time.
His first goal, scored in the 91st minute, was heartbreaking enough. The striker got free of his man at a corner to head in, denying Villa their first league win since February.
However, the second, coming in the 93rd minutes, summed up Villa's season as their rot of losses was extended for yet another game. The ball fell kindly to Watford's captain on the edge of the area, and he made no mistake by rifling in from 18 yards.