No team has conceded more top-flight home goals than the 26 Watford have shipped, and when Oumar Niasse inadvertently hit the woodwork in the first half, the Vicarage Road crowd would have been forgiven for expecting another difficult examination for their defence.
But, in a game in which opportunities were extremely limited, Deeney took his with aplomb 11 minutes from time to light up an otherwise disappointing spectacle.
Jordan Pickford had previously produced a fine save to deny Kiko Femenia, who had seen the Everton goalkeeper's clearance deflect off Deeney and into his path.
However, he could do little to stop the Watford captain from settling the contest as the forward rifled a stunning finish into the top-right corner.
Sam Allardyce's visitors had no response as Javi Gracia claimed his second win as Watford manager, moving them on to 33 points and into the top 10, just one point and one place behind Everton.
27 - Troy Deeney scored a goal from open play for the first time in his last 27 Premier League games (v West Brom April 2017). Thumped.— OptaJoe (@OptaJoe) February 24, 2018
Everton had the best chance of the first half when Niasse saw his low cross deflected onto the base of the near post following a quick counter.
From there chances proved few and far between in the opening 45 minutes, with the even nature of the contest reflecting the two teams' relative proximity in the table.
Sebastian Prodl and Michael Keane each wasted opportunities after the restart, both defenders heading off target at either end as the game became slightly more open.
Deeney then forced Pickford into action, but his save from the Watford striker's header was still relatively comfortable as defences continued to dominate.
Cenk Tosun, still yet to score for Everton since his January move from Besiktas, was brought on for Niasse in the second half in an attempt from Allardyce to spark the game into life.
But one of the chief creative presences on the pitch was then withdrawn as former Everton playmaker Gerard Deulofeu limped off after the hour.
Wayne Rooney fired way over on the volley before Pickford had to dive to his left to deny substitute Femenia after Deeney had partially blocked his clearance.
Yet there was an unexpected twist as Stefano Okaka pulled the ball back for Deeney to turn and lash beyond the helpless Pickford, who prevented the scoreline from being more comfortable for the hosts with a fine save from Okaka.
A remarkable late equaliser almost arrived deep in stoppage time as Pickford charged up for a corner and headed into the path of Dominic Calvert-Lewin, but the substitute could not scramble the ball in as Everton's miserable away record extended to one win from 22 top-flight games.
Key Opta Stats:
- Watford kept a clean sheet at Vicarage Road for the first time in their last eight top-flight games.
- They enjoyed only a third win over Everton in their last 25 meetings in all competitions (D3 L19).
- After picking up 10 points in his first four Premier League games as Everton boss, Sam Allardyce has seen his side accrue just nine in the last 10.
- Watford had to wait until the 55th-minute to register their first shot on target of the game, via a Troy Deeney effort (there had only been one before that from Everton).