The Baggies, whose losing run at Vicarage Road stretches back to 2007, now find themselves eight points adrift of safety at the foot of the table.
Deeney's goal arrived 13 minutes from time, as the skipper fired high beyond Ben Foster once slipped clean through to mark his 300th league appearance for the club in style.
Seeking three successive home wins for the first time in close to a year, Watford had an early scare as Adrian Mariappa was needed to produce a big block inside the box.
Mariappa made an impact at the other end, too, glancing on a corner and seeing the ball cleared away on the West Brom line before it could find the far corner.
Sebastian Prodl then failed to find the target when leaping to meet a set piece, ensuring that a quiet first half ended all square, though West Brom were quick out of the block for the second half.
Richarlison was not too far from converting with an acrobatic attempt effort prior to the hour mark, while Rondon once again squandered a good opening following a Jay Rodriguez delivery from the left.
Some big defending from Janmaat thwarted Rodriguez as the game burst well into life, before the striker was kept out by Karnezis's save 60 seconds later.
West Brom could not create any further chances, meaning a fifth successive league loss - their worst run of form for seven years - to cut them further adrift at the bottom.
WATFORD (4-2-3-1): Karnezis; Janmaat, Prodl, Mariappa, Holebas (Britos 95'); Doucoure, Capoue; Carrillo (Hughes 66'), Pereyra, Richarlison (Okaka 54'); Deeney
WEST BROMWICH ALBION (4-2-3-1): Foster; Dawson, Hegazi, Evans, Gibbs; Krychowiak (McClean 81'), Livermore (Field 84'); Rodriguez (Burke 87'), Phillips, Brunt; Rondon