Reading finally dashed any hopes Cardiff had of making the play-offs after a match that saw three different referees.
Appointed official Mark Warren left the field in the 35th minute and it was when play restarted with Steve Hadgood in charge that the Royals opened the scoring.
Play began with a corner to Reading and Cardiff were caught cold as Ivar Ingimarsson nodded the visitors ahead in the 39th minute.
Robert Earnshaw quickly levelled the scores three minutes later, but in time added on for the referee's changeover another header, this time from Dave Kitson, put Reading in front.
Bluebirds debutant loan signing Lee Bullock levelled up the scored once again in the 72nd minute, but three minutes later Habgood was forced to leave the field with another muscle pull and Richard Smith took over the whistle.
In time added on for the second changeover Reading substitute Dean Morgan was given a free header at the far post to earn all three points for the visitors.
"We showed a lot of spirit particularly after losing two players through illness in the last 24 hours," said Royals boss Steve Coppell.
"I think the delays with the referees helped us as we scored the opener straight from the restart. It was important that we started well and kept the home crowd quiet."Cardiff manager Lennie Lawrence was dismayed at the way his defence allowed three headers to win the game.
"We lost because of a total inability to defend high balls in the area. It's a bit harsh to lose in that manner, but we looked shaky in our own box.
"We lost the game not because we are missing three regulars, but because we failed to deal with an aerial threat."