Young headed home on 55 minutes after Shane Supple had palmed Marlon King's header on to the crossbar and Ipswich never looked like getting back into it.
The home side produced a shambolic display which left a band of around 50 home supporters chanting for the head of chairman David Sheepshanks after the final whistle.
Ipswich were dealt a blow before kick-off when Wales Under-21 international Lewis Price had to drop out with a cold, with Irish youth international Supple stepping in.
He made a nervy start, handling outside the area to give Watford a free-kick in a dangerous area, which Paul Devlin swung in for Jay Demerit to head over.
Adam Proudlock lifted a shot well over from Jay McEveley's low cross before a Young free-kick found Clarke Carlisle whose glancing header was cleanly gathered by the diving Supple.
Town came close midway through the half when Jim Magilton and Nicky Forster combined, the latter crossing for Darren Currie, who cleverly escaped two challenges before firing narrowly across goal.
Matt Richards fluffed a volley from a Magilton cross and then the game entered a scrappy period in which both Matthew Spring, Carlisle and Richard Naylor were cautioned by demoted Premiership official Andy D'Urso.
D'Urso showed just why he has been banished from the top-flight with a series of contradictory decisions, including sparing Spring despite the visiting midfielder committing two further bookable fouls after his initial caution.
As the half entered stoppage time, King had an effort deflect wide off McEveley before Richards charged down a Darius Henderson shot and Supple got down well to hold Spring's follow-up.
Spring and Richards shot over early in the second half at either end, before the game turned in a 60-second period.
What turned out to be Town's only on-target effort, a scuffed shot from Proudlock after a huge Supple clearance bounced over Carlisle, was immediately followed by Watford's winning goal at the other end.
Devlin's right-wing cross produced a bullet header from King which Supple palmed on to his crossbar, but as Spring went for the loose ball, in the confusion it ran free to Young who stooped to nod into the empty net for his ninth goal of the season.
Town boss Joe Royle responded by sending on Sam Parkin and Dean Bowditch for Magilton and Proudlock, but both are struggling for confidence - Parkin without a home goal since his summer move from Swindon and Bowditch having gone goalless for a full year.
Supple did well to save a downward header from Henderson following a Lloyd Doyley cross and the same player had an effort blocked after Jason De Vos, up from the back for a long throw, seized on a loose ball but dragged his shot wide.
Watford thought they had sealed the point on 74 minutes when Young swung in another of his dangerous set-pieces for Demerit to head in, but D'Urso got this decision right as he spotted a clear push.
Gavin Mahon shot over after robbing Currie and at this point the only chance of seeing another goal looked to be if the visitors got one, with Town having no ideas other than aimlessly punting the ball forward in the hope of getting a fortunate break.
James Chambers and Doyley were booked for Watford - making it four visiting players in total - before Town almost gained a freak equaliser when Carlisle's back header was only gathered at full-stretch by Ben Foster.
That was the last chance at either end as Watford claimed a well-deserved victory, while the home side may be looking at more of a relegation battle than a push for promotion on this evidence.