Debut-making striker Jason Byrne came off the bench to give Cardiff their first win in 13 games.
Byrne is top scorer in the Eircom League for the past four years
Bluebird fans banned from Molineux missed Mike Chopra breaking his seven game drought in style with an airborne chip over Matt Murray from 20 yards.
Craig Davies hit the post and had a goal disallowed before his surging run brought the equaliser, setting up Seyi George Olofinjana from short range.
With two minutes to go Chopra slid a pass to Byrne who blasted in the goal.
Cardiff will be troubled by an injury to captain Darren Purse, though, who limped off before half time with a back injury.
606 DEBATE: Give your thoughts on the match
Wolves manager Mick McCarthy:
"How do you think any manager would feel after watching his team run riot, create chance after chance after chance, hit the post and have a goal disallowed but still lose the game?
"I feel robbed when I should be waxing lyrical about having scored four or five goals. We will never play any better than that but we just have to finish off those chances.
"Craig Davies had a perfectly good goal disallowed for a foul on the goalkeeper, but I did not see a foul.
"And was Michael Chopra offside for the first goal? Was it first phase? Was it second phase?
"I do not know any more because the law of offside is an ass. Overall it was a terrific performance from us but the atmosphere was rubbish."
Cardiff manager Dave Jones:
"It was ironic our fans were not at the ground, but we got them just reward.
"In all my time when I was manager of Wolves and bringing opposition teams to Molineux I have never felt an atmosphere like it, it was dead.
"Losing Darren Purse is a big blow because he is an experienced player and the one who keeps what is a young defensive line together.
"He has damaged discs in his back and it is too early to say how serious the problem is but we will get him off for tests as soon as we can.
"But Darren is a strong character and hopefully the discs can click straight back in."
Wolverhampton: Murray, Little, Neill Collins, Fleming, Clapham, Kightly, Olofinjana, Henry, Potter, McIndoe (Johnson 82), Craig Davies (Ward 80).
Subs Not Used: Oakes, Mark Davies, Lee Collins.
Goals: Olofinjana 58.
Cardiff: Alexander, McNaughton, Purse (Johnson 41), Loovens, Ledley, Parry, Scimeca, McPhail, Whittingham (Flood 74), Thompson (Byrne 62), Chopra.
Subs Not Used: Forde, Campbell.
Goals: Chopra 27, Byrne 88.
Ref: J Moss (West Yorkshire).