Substitute Nicky Barmby scored the winner as Hull leapt above Cardiff in the Championship following victory at the KC Stadium.
The 37-year-old applied the simplest of touches from Robbie Brady's cross only a minute after coming onto the field.
Matty Fryatt had found the target from from six yards to give the home side the lead on 39 minutes.
Cardiff drew level when league debutant Joe Ralls scored with a volley on 61 minutes before Barmby's winner.
Hull handed a league debut to Austrian winger Martin Pusic while Cardiff kept faith with the side which had started the win against Southampton in midweek.
Among the Cardiff substitutes was 17-year-old striker Ralls, who had only signed his first professional contract with the club 48 hours earlier.
Only two points separated the sides in the Championship table prior to the match with Cardiff sixth and Hull one place behind them in seventh.
The visitors forced the game's first corner after only 40 seconds, but it was Hull who had the early chances to take the lead.
On loan Manchester United winger Robbie Brady forced goalkeeper David Marshall into a save with a thumping 25-yard free-kick before Corry Evans volleyed just over the bar.
Cardiff's injury woes continued when Kenny Miller was forced off with an injury after nine minutes with Ralls coming on to make his Championship debut.
Without Miller, the Bluebirds looking lightweight up front and although Filip Kiss and Peter Whittingham had efforts they had to wait until the 30th minute for their first real effort on goal when Anthony Gerrard headed wide from Whittingham's corner.
Hull were taking control of the game and Waghorn went close with a header following Liam Rosenior's cross before they went ahead six minutes before half-time.
Pusic played the ball into the penalty area from the left and Fryatt wriggled clear of his marker to squeeze a low shot between Marshall and the inside post for his second goal of the season.
Having gone ahead, Hull were again on the attack two minutes later with Waghorn fending off Darcy Blake and Kevin McNaughton before firing over the crossbar.
Slovenian midfielder Robert Koren flashed a 25-yard volley wide after the break and Fryatt saw his shot from inside the area well saved by Marshall.
But against the run of play Cardiff were back in the game on 62 minutes and it was debutant Ralls who scored with a spectacular strike.
Kevin McNaughton found Ralls with a pass from his own half and the youngster carried the ball into space towards the edge of the area before unleashing an unstoppable shot.
Within a minute Brady went close to restoring Hull's lead with Cardiff's Whittingham also trying his luck from long range.
Cardiff thought they had been awarded a penalty only for the referee to deem Filip Kiss had strayed into an offside position.
The home side made a change on 70 minutes with Barmby replacing Pusic, and the former England striker made an immediate impact.
A minute later, from Brady's cross from the right, Barmby despatched a left-footed finish into the bottom corner to score what would prove to be the winner.
Despite Cardiff's valiant efforts they could not avoid their second Championship defeat of the season as Hull extended their unbeaten run to six matches.