A very dominant and fluid Royals performance was not justly rewarded at Elland Road tonight as Chris Wood's first half finish and an injury time penalty from Souleymane Doukara separated the sides in Yorkshire, handing Garry Monk's men all three points.
The Royals earned 77% of possession on the night, while United didn't win a single corner, but the hosts capitalised on their chance in 19th minute and made sure of the victory when Charlie Taylor won a controversial penalty at the death.
Manager Jaap Stam made one change to the side that beat Sheffield Wednesday at the weekend, bringing Liam Kelly into midfield with Jordan Obita missing out. Callum Harriott and Sandro Wieser came into the squad to take a place on the substitutes bench, with Joseph Mendes not included.
Kemar Roofe scurried down the right flank to cause some early concern for the Royals defence, coming inside before seeing his low cross smothered by the sprawling body of Ali Al Habsi.
But the Royals soon settled into a rhythm and good battling from Dom Samuel seemed to have set up a shooting opportunity for Roy Beerens, until the whistle sounded for a foul by the striker in winning the ball from Pontus Jansson on the edge of the box.
Superb footwork from Hadi Sacko saw him cut inside two men on the right and tee up Roofe for a shot that he skied over the crossbar to the Royals' relief. But Reading came close moments later when Kelly threaded the ball into the run of McCleary who saw two shots charged down before Van den Berg's follow-up was parried by Leeds keeper Rob Green.
And the best chance of the half so far fell to top scorer Garath McCleary. Two lovely threaded balls through the Leeds midfield and defence found McCleary who scrapped his way past the last man. Through on goal, he looked to square to the supporting Samuel but the pass was cut out and Leeds eventually cleared.
Reading were made to pay very soon after. A dangerous run into the box from Sacko was cut scrappily into the middle of the box and it fell kindly for Chris Wood who reacted quickest to leather it high into the roof of the Royals' net.
The goalscorer had to make way on the half hour, replaced by Liam Bridcutt after picking up a knock. But Leeds were looking for a second and Dallas led a break away only to fire harmlessly over.
Two pieces of good defending from Jansson denied McCleary shooting opportunities at the other end and Jaap Stam's men were controlling possession and creating chances of their own as they sought an equaliser.
And Samuel just couldn't get enough on a glancing header at the near post when Beerens crossed from a good position on the left - although it looked like Green gathered the ball in from a back pass as the Leeds defence hurriedly mopped up.
A half chance presented itself to Samuel moments later after Reading had won the ball back through high pressing on the right and Kelly had slotted an early ball into the striker's feet - but again the United defence recovered to deny Samuel a shot.
Yet for all the visitors' dominance in possession, Garry Monk's men went into the dressing room with a goal's advantage.
Half-time: Leeds 1-0 Reading
Al Habsi had to collect dangerous crosses from Taylor on the left and then Sacko on the right early in the second half, but Liam Kelly did well to turn his man at the other end - driving low wide of Green from 22 yards out but also wide of the bottom left corner.
Samuel won a free kick soon after but the wall did its job against Kelly's set piece, then Sacko stole possession from Blackett on the right wing to cross low into the six yard box where Souleymane Doukara slid in but couldn't toe it goalwards.
Ten minutes gone and a Beerens cross from the left found the head of McCleary but the winger headed a difficult chance over the crossbar. Then Yann Kermorgant's first touch after coming off the bench saw him win the ball ahead of Jansson and feed Kelly, who couldn't quite take it in his stride and into the Leeds box - a one-two was read and Leeds had the ball back.
Reading continued to play the patient game and then almost unlocked their hosts with a quick counter, Kermorgant feeding Beerens to turned onto his left boot and forced a fingertip save from Green with a powerful drive.
A tired Leeds were sitting deeper and the Royals were running out of time. But they kept probing, McCleary's floated corner met by the head of Kermorgant and McShane tried to turn it home from close range only for Green to push it around his post.
Another lovely move almost unlocked the Leeds defence, this time Kermorgant dinking the ball over the top for Kelly who took a sublime first touch but saw his toe poke saved - and the offside flag ruled it wouldn't have counted anyway.
It was all Reading, pressing and pressing for a goal they deserved. Blackett pulled the ball back for McCleary whose shot was charged down, then Beerens' follow up was blocked. Stam brought Jake Cooper on for the final minutes as the visitors looked for a late, late equaliser.
But in injury time, Taylor scurried inside from the left and went to ground inside the box to win a last gasp penalty for the home side instead. And Doukara swept home to put the game to bed.
Meite had a shot cleared off the line with the last kick of the game, denying the substitute a consolation, but it was Leeds fans celebrating at the sound of the final whistle.
Full-time: Leeds 2-0 Reading
Leeds United: Green, Ayling, Taylor, Jansson, Bartley, Vieira, Doukara, Dallas (Grimes 83), Sacko, Roofe (Mowatt 70), Wood (Bridcutt 34).
Subs: Silvestri, Wilks, Cooper, Berardi.
Goals: Wood (18), Doukara (90 pen)
Reading: Al-Habsi, Gunter, Blackett, McShane (c), L.Moore, Van den Berg, Kelly (Cooper 87), Evans (Meite 78), Beerens, McCleary, Samuel (Kermorgant 62).
Subs: S.Moore, Watson, Wieser, Harriott.