Ryan Hall had handed Leeds the lead with a sweetly-struck free-kick on the stroke of half-time before Chris Dawson extend the advantage in the 63rd minute.
Blues sub Reece Hales, playing back at the stadium where he made his first-team bow earlier this season, threatened a comeback by pulling a goal back in the 69th minute. However Lewis Walters, celebrating his first pro deal, wrapped up a deserved victory for The Whites in the 89th minute.
Senior defender Pablo Ibanez made his return to competitive action following a groin injury while goalkeeper Colin Doyle was the only other over-aged player to start for the away side. Blues also had Tottenham Hotspur trialist Jack Munns playing up top off Akwasi Asante.
Despite facing a series of chances from a lively and attacking Leeds side, resolute defending from Blues looked to have done enough to ensure that the game remained all square at the break.
Walters and Jason Pearce both saw efforts hooked off the line while Habib Habibou looked a constant threat with a series of forward forays that were only pulled back by the linesman’s raised flag.
Blues’ only attacking chance of note in the first-half came in the 37th minute when Asante latched on to a Munns throughball but the striker took the ball too far allowing Leeds ‘keeper Eric Grimes to charge out and thwart the move.
Leeds took the lead with half-time looming. Habibou was fouled on the edge of the Blues area and Hall stepped up to smartly curl home the free-kick with his left foot.
The Yorkshire side continued in the same vein after the break; Hall picking out the run of Pearce in the 49th minute only for his header to bounce dangerously across the face of Doyle’s goal and wide.
James Fry was introduced to proceedings just before the hour mark and the young centre-half was immediately called into action; tracking back well to deny Habibou as the striker was preparing to pull the trigger just inside the Blues box.
However, it wasn’t long until Habibou was on the rampage again and on this occasion there was little Fry could do as the rangy forward teed up Dawson for a fine low finish from 18 yards.
Hales replaced trialist Munns and went on to make an immediate impact. Asante showed good strength to tee up his striker partner to fire home from the left side of the six yard box.
The impressive Dawson had a glorious chance to double his tally but scooped an effort over from six yard, after being teed up by Lewis Turner, before sending a long range effort fizzing just past the right post.
Walters then killed the game off in the last minute as he used his pace to race free of the Blues defence and fire beyond the hapless Doyle.
Blues U21s: Colin Doyle; Ryan Higgins, Amari’i Bell, Olly Lee, Pablo Ibanez (James Fry 58), Emmitt Delfouneso, Charlee Adams, Liam Truslove (Eddy Gnahore 69), Akwasi Asante, Jack Munns (Reece Hales. 65), Koby Arthur.
Subs not used: Nick Townsend, Graham Hutchison.