The Premier League outfit made hard work of seeing off their hosts, Will Hughes giving them a first-half lead before Deeney was introduced late on to secure a 2-0 victory in Surrey.
A massive 110 places separated the two clubs in the football pyramid as they took to the pitch at the Laithwaite Community Stadium – but National League South promotion hopefuls Woking gave a spirited performance.
Their manager Alan Dowson, joined in the dugout by coach and Sky Sports commentator Martin Tyler, said before the game that it was "ridiculous" to suggest his side could cause a shock.
In truth they never looked like pulling off a giant-killing but they also held their own at times as Watford laboured to build on their lead.
Javi Gracia changed his entire team from that which drew 3-3 at Bournemouth in their last Premier League game, with Deeney on the bench and midfielder Abdoulaye Doucoure – linked with a move to Paris St Germain – not involved at all.
Woking, meanwhile, were without the influential Max Kretzschmar as they showed two alterations from their last outing – a 3-0 win at Hampton and Richmond on New Year's Day.
Domingos Quina saw an early shot blocked as the top-flight visitors unsurprisingly dominated early possession.
Adalberto Penaranda, who moved to Vicarage Road in 2016 but has been out on loan at Granada, Udinese and Malaga in the mean time, came close to marking his Watford debut with a goal but his effort was turned behind.
Woking then enjoyed a flurry of attacks as Hornets full-backs Adam Masina and Daryl Janmaat had to be alert to prevent clear-cut opportunities on Heurelho Gomes' goal.
Craig Ross had no such protection at the other end as Watford took the lead with 13 minutes on the clock.
Masina saw a close-range attempt turned behind by Ross but a short corner routine found Hughes unmarked and the midfielder made no mistake as he rifled the visitors in front.
Isaac Success was cautioned for diving before forcing a smart stop from Ross, with Ben Gerring's header registering Woking's first effort on target at the midway point of the first half.
Watford were a threat whenever they got the ball in and around the Woking penalty area and it was Tom Cleverley, making his first start in almost a year following Achilles surgery, who clattered a free-kick against the crossbar after Penaranda had been fouled.
The chances dried up in a stale second half, with Woking sticking to their defensive duties with diligence as Watford toiled to break them down for a second time.
That changed as Gracia responded by introducing Deeney with 19 minutes remaining – and he soon made sure of Watford's place in the fourth round.
The ball was switched to fellow substitute Ken Sema, who burst into the Woking box before crossing for Deeney to tap home from point-blank range and seal the tie.
There was still time for Deeney to have a header cleared off the line while Harvey Bradbury should have halved the arrears in the closing stages only to send his own header well off target.