Neil Cox's penalty after 14 minutes separated the sides before Reading's continued push for an equaliser allowed the visitors to emphatically underline the scoreline.
Striker Hameur Bouazza put the tie out of Reading's reach with a snap-shot from the edge of the area as the game ticked into stoppage-time.
And Reading, who had started their campaign with five successive home league wins, saw their night take another ugly turn when defender Ivar Ingimarsson turned substitute Andy Ferrell's cross into his own net in the dying seconds.
The scoreline was rough on Reading, who had created countless first-half chances only to trail to Cox's 14th-minute spot kick.
Steve Coppell, facing his friend and former Crystal Palace ally Ray Lewington for the first of two games in five days, saw his Reading side start brightly as Shaun Goater set up his strike partner Dave Kitson for a shot that flew just across the face of goal.
But Watford snatched the lead when Adrian Williams was outrun by Bruce Dyer and stuck out a boot to concede a penalty.
Cox confidently stroked home the spot-kick, with what proved to be Watford's only shot on target in the opening 80 minutes of the game.
Reading fought hard for an equaliser and Goater was unlucky not to score his second Carling Cup goal of the campaign when he twice struck the crossbar in the space of 17 first-half minutes.
The former Manchester City striker crashed a header against the woodwork from a corner earned by his own deflected shot.
Then, on the stroke of half-time, Richard Lee's uncertainty allowed the Bermudan striker to run into space and chip a shot that beat Cox on the line but smacked against the bar once more.
The home side pushed more and more men forward in search of an equaliser in the second half, but rarely threatened to loosen Watford's grip on the game.
Substitute Lloyd Owusu should have levelled six minutes from time, but somehow sidefooted wide with the goal at his mercy.
And that miss was punished in the dying moments when Bouazza took advantage of the increasing gaps in Reading's defence to drill home a low shot into the far corner.
Ferrell put the icing on the cake with an injury-time cut-back that cannoned against the helpless Ingimarsson and rolled past Marcus Hahnemann into the Reading net.