Watford were denied a deserved point after Cardiff scored from a controversial penalty with the final kick of the game.
Tommy Smith returned from injury to score from the spot in the ninth minute against the side that tried to sign him in January.
Smith's goal was soon canceled out by Jay Bothroyd and it looked as though the Hornets were about to pick up a point against promotion-chasers Cardiff.
But after the three minutes of injury time had already passed, Ross Jenkins was adjudged to have handled on the line and Ross McCormack scored from the spot.
It is the second time in two games that Watford have conceded penalties deep into time added on.
Watford started brightly and were passing the ball well but it was a tricky run in the ninth minute by Jobi McAnuff, from inside his own half, which ended up in the former Cardiff man being brought down in the box.
Smith, playing for the first time since Kelly Youga forced him off through injury against Charlton, coolly slotted the ball past Stuart Taylor into the 'keeper's bottom left to make it 1-0.
Both sides were trying to play attractive football and Cardiff had a couple of chances soon after the opener.
After Paul Parry had failed to get any power on Chris Burke's cross, Jay Bothroyd's neat flick put Joe Ledley in but the Welshman's shot to the near post was easily saved by Scott Loach.
There was a doubt over whether Bothroyd would be fit to play but the former Coventry man equalised in the 15th minute.
Burke's cross was not cleared and the ball fell to Bothroyd, who volleyed into the bottom corner.
Tamas Priskin was causing problems and Cardiff's Roger Johnson needed to make an excellent diving challenge to stop the striker from shooting.
The Hungarian then beat Gabor Gyepes out right before smashing in a dangerous cross which Johnson just beat Smith to in the six yard box.
Ledley looked lively in the middle of the park and again a one-two with Bothroyd created another chance for Cardiff, but Jenkins' slide tackle stopped Ross McCormack from shooting.
The Scottish striker had another chance moments later when Kevin McNaughton's free kick was not cleared and McCormack flashed a volley wide of the near post.
The Cardiff striker saw another effort go wide when he failed to make decent contact on Tony Capaldi's cross.
Watford were looking to break when possible and another McAnuff run resulted in Priskin being brought down 20 yards out but Don Cowie's low free kick went comfortably wide.
After Bothroyd was brought down 20 yards out, McCormack hit a free kick into the wall.
But the dangerous Ledley should have scored shortly before half time when he was not tracked into the box by Ross Jenkins.
From eight yards out and with the goal at his mercy Ledley decided to try and pass to Johnson rather than shoot and Doyley cut out the pass.
Loach held a curling McCormack shot and Cowie fired a half volley over the bar before the break but the sides went in at one a piece.
McAnuff again started the half well and would have been through on goal had McNaughton not brought him down.
However, Cowie's free kick was cleared and Cardiff broke quickly but McCormack headed wide from eight yards out.
Former Wycombe defender Johnson had a header saved by Loach moments later as Cardiff started the second half as they finish the first; on top.
The game was a bit scrappy for a while and the Cardiff fans were becoming slightly restless as their side kept misplacing their passes.
Watford came back into the game more but were unable to create any chances.
It looked as though McCormack was set to shoot from 12 yards after Bothroyd beat Williamson in the air but the striker's touch was heavy and Mariappa cleared the ball.
Similarly, a neat interchange between McAnuff, Cork and Jenkins saw McNaughton just clear before Jenkins was about to shoot.
The game opened up around the hour mark and Watford had a quick break following a challenge from Cork but Smith's cross was cut out by the 'keeper.
A deflected Peter Whittingham shot led to a Cardiff corner, which although it was cleared, resulted in Johnson just heading wide a Burke cross.
Watford enjoyed a spell of possession in Cardiff's half but McAnuff's cross would not fall to Priskin.
Watford were on top in the later stages of the game and Cardiff were fortunate that a Smith cross was scuffed by a home defender into their keeper's arms and not to the feet of the nearby Priskin.
Some patient build-up from Watford then saw Cork head a Mariappa cross wide with two minutes to go.
The visiting side remained in charge in injury time but then Cardiff were given a penalty and scored with the last kick of the game.
City won a corner after Loach made an excellent save from a long-range effort by McCormack.
Johnson jumped highest at the resulting corner and his header was blocked on the line by a diving Jenkins but the referee adjudged the youngster had used his arm and pointed to the spot.
As on Saturday when Jon Harley was penalised, there was controversy but after consulting with his linesman, Andy Hall awarded the spot kick and McCormack dispatched calmly.
Cardiff: Taylor; McNaughton Gyepes, Johnson, Capaldi; Burke (Chopra 74), Ledley, McPhail, Parry (Whittingham 45); Bothroyd, McCormack. Subs: Rae, Johnson, Kennedy.
Watford: Loach; Mariappa, DeMerit, Mike Williamson, Doyley; McAnuff, Jenkins, Cork, Cowie; Smith, Priskin. Subs: Lee, Hoyte, Cauna, Parkes, Hoskins.
Bookings: Cork, (29, professional foul), Mariappa, (45, dangerous play), McNaughton (48, professional foul), McAnuff (79, dangerous tackle).
Referee: Andy Hall.
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