Marlon King scored in each half and strike-partner Darius Henderson piled on the agony for the Bluebirds who only had a late Cameron Jerome goal to appease the home fans.
City made one change to their starting line-up with Philip Mulryne taking over in midfield from Willie Boland.
Both sides took time to settle but it was the Hornets who struck first in the seventh minute when King wrong-footed City skipper Darren Purse before firing low and hard across Neil Alexander and into the far corner of the net.
King, on a season-long loan from Nottingham Forest, then rose above Purse to meet a cross from Paul Devlin but his header went wide of the post.
The Hornets should have doubled their lead in the 23rd minute when Dominic Blizzard outstripped Mulryne down the right. He cut inside and fired low into the six-yard box where Henderson was waiting, but his point-blank shot was parried by Alexander before being hacked clear by Jermaine Darlington.
The Bluebirds' first attempt on goal did not come until the 38th minute when, following a neat move involving Jerome and Darlingon, Jeff Whitley raced into the middle but he pulled his shot wide of the goal.
The visitors took advantage of yet another Purse slip and the ball was sent out to the on-rushing Deviln but Alexander went full-length to save.
There was a little more purpose about City after the restart and they were able to mount a couple of attacks, but it was Watford who had the first strike on goal in the 51st minute when Henderson headed tamely at Alexander.
He made no mistake one minute later, however, when he rose above Purse to head in a Deviln cross off the City skipper to increase the visitor's lead.
Cardiff's saviour against Leeds, Jason Koumas, entered the fray along with Alan Lee on the hour.
The changes made little difference to the Hornets and they put the game beyond Cardiff with a second strike by King in the 67th minute.
Gavin Mahon let fly from the right and the ball came off a City defender to the waiting King who rifled his shot into the net across Alexander.
With 10 minutes remaining Jermone chased a long ball down the middle rounded Watford keeper Ben Foster and stroked the ball into the empty net for a small consolation.