Stoke produced a stirring performance to claim their first win under Nathan Jones as Leeds ended a difficult week with a third defeat in four Sky Bet Championship games.
In the build-up to kick-off at the bet365 Stadium, the English Football League revealed 11 clubs had officially complained about Leeds spying on opposition teams.
And United have issues on the field too after centre-back Pontus Jansson was sent off on a day when nothing went right for Marcelo Bielsa's team until Ezgjan Alioski made it 2-1 with the last kick of the game.
Sam Clucas brought an uneventful match to life just after the restart by rifling home the opener and Joe Allen finished off 10-man Leeds.
Leeds remain top of the table but their lead is only one point and they will now await the EFL's verdict on Bielsa's pre-game habit.
Buoyed by last week's dominant win over Derby, Leeds dominated the opening exchanges with Pablo Hernandez fizzing a 20-yard shot just wide inside two minutes and then scuffing another effort wide.
Stoke slowly grew into the game and twice forced Bailey Peacock-Farrell into saves, Allen shooting straight at the Leeds goalkeeper from the edge of the box and Peter Etebo going closer from a free-kick.
Leeds right-back Luke Ayling turned a Benik Afobe cross wide of his own goal and Hernandez failed to trouble Jack Butland with a curling shot as both sides struggled to create a genuine opportunity.
Half-time gave the teams a chance to regroup and it was Stoke who took the initiative aided by some poor Leeds defending.
The visitors failed to prevent a cross coming in from the right and made a mess of trying to clear it, leaving Clucas with an invitation to drill a half-volley into the bottom corner.
Stoke immediately retreated but Leeds were struggling to break them down and nearly conceded a second when Ashley Williams found some space at the back post from a corner, only to stab a shot harmlessly at Peacock-Farrell.
Hernandez had a penalty appeal waved away and Jansson headed well over as Leeds grew more frustrated.
United were left with an improbable task when the Swedish centre-back was sent off after receiving a second yellow card for slowing Afobe down on his way to goal.
Substitute Tyler Roberts forced Butland into a low save and the England goalkeeper had to be at his best to keep out Ayling's header from a Hernandez corner.
Allen struck the telling blow three minutes from time by turning home James McClean's low cross and Stoke celebrated their first victory since December 22, despite Alioski's stoppage-time effort.
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