Both sides found chances hard to come by for much of the first half, but the deadlock was broken with four minutes left until the break. Bolton failed to clear their lines, allowing Craig Noone to fire the ball through a crowd of players and past the unsighted Adam Bogdan.
They thought they had found the equaliser just after the hour mark when David N'Gog converted with his first touch, but it was ruled out for offside.
N'Gog did have a part to play in Bolton's eventual equaliser, however, winning the penalty that Martin Petrov stepped up to score.
N'Gog continued to terrorise the Cardiff defence, giving his side the lead just five minutes later by diverting Sam Ricketts's shot past the keeper.
The former Liverpool man capped off an eventful cameo appearance in the 90th minute by picking up a second yellow for a late tackle, reducing his side to ten men, but Bolton managed to hold on to claim all three points.