Mowatt's goal - his first in seven months - gave Leeds a first home win in eight months and a first victory over Cardiff in 31 and a half years. For boss Steve Evans, it was a first three points in charge of the Sky Bet Championship side.
Midfielder Mowatt - largely out of sorts so far this season - took aim with 63 minutes on the clock and left David Marshall flat-footed in the Cardiff goal.
None of Leeds' matchday squad were even born the last time United beat Cardiff in February 1984, but the main statistic that will concern Evans is that his reign at Elland Road now boasts a win at the fourth attempt.
It was going to take a special goal to break up the tedium of this clash too, with quality moments few and far between in the main.
The only glimmer of action in the opening exchanges was a half-hearted penalty appeal from Leeds striker Mirco Antenucci, and the action rarely got better than that before the break.
Leeds' Stuart Dallas had two efforts, one which dragged wide and another which David Marshall beat away, and if anyone could claim half-time bragging rights it was the home side.
Cardiff's attacking threat could not have been lower during the first half and they at least upped it at the start of the second, Marco Silvestri making his first save as he scrambled away Sean Morrison's deflected header.
Russell Slade's men failed to turn that into an extended spell of pressure, though, and Leeds - in particular Mowatt - took advantage.
Little was on when the ball landed at his feet midway through the Cardiff half, but he took a touch and, with little other option, found the top-right corner with impressive accuracy.
The goal was the signal for Cardiff to wake up. Joe Mason forced Silvestri to turn a low grass-cutter around the post and then held on to a Morrison header from the subsequent corner.
A second goal should have been Leeds' and would have were it not for an inexplicable miss from Chris Wood. He latched on to Lee Peltier's weak back-pass and, after rounding Marshall, failed to find the open goal.
In the end it was not needed and Leeds were able to see out the win.