The midfielder scored in the third minute as Middlesbrough, who entered the day’s early kick-off one point clear at the top of the table, fell to a first home defeat since August.
Aitor Karanka’s men headed into the afternoon’s early game brimming with confidence having risen above Derby and Bournemouth with a 1-1 draw at Birmingham on Wednesday.
But they got off to a terrible start when Mowatt put the visitors ahead with a deflected strike.
Middlesbrough responded well but, despite creating a glut of chances, they could not find a way past the dogged rearguard led by Leeds skipper Sol Bamba, while goalkeeper Marco Silvestri made a string of fine saves.
Middlesbrough’s pre-match position did not stop Karanka continuing his rotation policy, with six changes made to the side that started in midweek.
It was the sole enforced alteration that proved Boro’s undoing, though, as Leeds took an immediate lead.
Tomas Mejias, in the XI because Dimi Konstantopoulos was serving a suspension for the red card he received against the Blues, saw a poor throw-out intercepted by Lewis Cook.
The midfielder took full advantage, pulling back for Mowatt to fire into the bottom corner via a deflection.
Middlesbrough almost bounced back immediately, only for Jelle Vossen to fluff his lines having been picked out by Grant Leadbitter’s well-worked free-kick.
The home side looked the most likely to score thereafter, with Kike and Vossen drawing smart saves from Silvestri.
Vossen then went agonisingly close to levelling when Giuseppe Bellusci cleared off the line to deny the Belgian after good work from Kike and Adam Reach.
The onslaught showed few signs of halting as only last-ditch defending and excellent saves from Silvestri were able to deny Kike and Adam Clayton, keeping Leeds ahead at half-time.
Picking up where they left off, Middlesbrough applied further pressure following the interval, Kike seeing an effort turned around the post by Silvestri.
But Leeds issued a warning shot of their own moments later when Scott Wootton nodded James Murphy’s free-kick against the crossbar.
Any thoughts that his effort may herald a spell of visiting pressure were quickly extinguished, Silvestri again called into action by Kike and Albert Adomah.
Karanka introduced top-scorer Patrick Bamford midway through the second period in a bid to find an elusive equaliser. Yet even switching to 4-2-4 did not bring the desired goal, with Bamba denying Kike after a sublime move.
Frustration then turned to worry inside the Riverside as Vossen was stretchered off with what appeared to be a serious head injury.
That meant there were nine minutes of injury time, although Middlesbrough – down to 10 men having used three substitutes – could not force themselves level.