The hosts allowed Steven Caulker a free header from Peter Whittingham's corner for the opener, although substitute Bryan Ruiz levelled on the stroke of half time.
But the Bluebirds won it with Jordon Mutch's spectacular strike deep into injury time to leave the Cottagers rooted in the Premier League drop zone.
Jol's side also slumped to a last-gasp loss at Newcastle and also conceded an injury-time goal in the 1-1 home draw with West Brom, and the Fulham boss was left exasperated that it had happened again.
"You feel ashamed because it's in the dying seconds again. It happened against Newcastle, against West Brom, and it happens again," he told Sky Sports.
"You feel ashamed about the first goal as well because you talk about it, try to do something in training and they still got the clear header so it's very disappointing."
Jol was left to rue missed opportunities when his side improved after the break.
The Dutchman added: "You are 1-0 up against West Brom and then it is 1-1, it was not 4-0 or 5-0, it's disappointing that we can't win the game but we're always close.
"Today again, we were very close, 1-1, and you feel you had three or four opportunities to score and you didn't and then they score.
"So I can easily say that we lacked a little bit of luck but that is too easy."