The Spaniard said before the game that he felt unappreciated after steering the mid-table Hertfordshire club to Premier League safety and an FA Cup semi-final.
But the players clearly still believe in him and refused to accept defeat against a Villa side who twice led either side of halftime through Ciaran Clark and Jordan Ayew, the first time Villa have scored twice away since September.
In between Almen Abdi had equalised for Watford before Deeney settled matters late on with a close-range header after 90 minutes and a right-foot strike three minutes later that left Villa equalling a club record of 11 straight league defeats. .