Swansea City made eight changes from the side that won the league meeting just two days ago, while Watford showed five changes.
A Ferrie Bodde free-kick that took a deflection had Richard Lee scrambling across goal after just 90 seconds and, in the tenth minute, Guillem Bauza threaded a pass out wide to Febian Brandy, but his snapshot went across goal.
Five minutes later, Tamas Priskin had a clear header from a corner but he struck it wide while unmarked.
Then Tommy Smith flipped Jobi McAnuff through, but his shot lacked power.
The Hornets continued to press and, in the 21st minute, they took the lead when Smith pushed a pass to Williamson, who raced on before powering a shot into the corner of the net.
Watford had the better of the exchanges but, though Priskin and McAnuff went close, they were unable to build on their lead as the half drew to a close.
A long throw by Alan Tate in the 53rd minute should have brought the equaliser but, with only the keeper to beat, Gorka Pintado misjudged the bounce of the ball and the chance was lost.
The Swans made a double substitution in the 57th minute bringing Jordi Gomez and Mark Gower on to increase their attacking options.
Gomez was soon in the action with a stinging shot that Lee gathered low down as the Swans pressed for the equaliser.
With five minutes remaining, Jason Scotland was added to the fray as the Swans threw everyone forward.
They won a free-kick just outside the area with two minutes of ordinary time remaining, but the shot from Gomez hit the inside of Lee's post and rebounded to safety.
Despite a further five minutes of added time, the Swans were unable to get back on terms and slipped out of the Carling Cup in disappointing style.