The Bluebirds looked devoid of ideas for most of the contest and were dealt a late blow when North End skipper Clarke found a way through for the only goal of the game.
A third defeat on the bounce for Neil Warnock's men for the first time in 15 months leaves them third in the Championship table on goal difference, with the two sides directly above them facing off tomorrow evening.
Chances were at a premium in the first half at the Cardiff City Stadium, with neither side managing a shot on target.
The visitors were seeing more of the ball but doing little with it, as Paul Gallagher blasted a free kick into the wall before the follow-up was swept clear.
There was also a small chance for Kenneth Zohore to make it two goals in two games, but he saw his attempt from a good position blocked aside, while Lee Tomlin glanced a header into the hands of Chris Maxwell soon after the restart.
Cardiff started to build some momentum as the second half went on, with Nathaniel Mendez-Laing the latest player to squander a good opening, though PNE were also looking lively at times and came close through a rising Horgan shot.
The visitors, now unbeaten in nine matches, were given a slight scare 20 minutes from time when Maxwell's attempted clearance ricocheted off Junior Hoilett and went behind for a goal kick.
Preston would go on to take all three points from the match, though, as Etheridge fumbled the ball away and Clarke was there to head it over the line.
A late chance came and went for substitute Rhys Healey, who could not get the better of Maxwell, meaning a first home defeat in nine against North End for the Bluebirds.
Cardiff City (4-3-3): Etheridge; Paterson, Manga, Bamba, Peltier; Damour, Ralls, Tomlin (Healey 76'); Feeney (Hoilett 64'), Zohore (Bogle 83'), Mendez-Laing
Preston North End (4-2-3-1): Maxwell; Clarke, Huntington, Davies, Cunningham (Woods 84'); Gallagher (Harrop 68'), Pearson; Barkhuizen, Browne, Horgan (Robinson 69'); Hugill