The Clarets fell at their first hurdle of the FA Youth Cup on a disappointing night in South-West London.
With the competition resuming following a Covid-enforced pause, Burnley belatedly started out with the prospect of a home tie against Tottenham to come in round four.
But it was Wimbledon who seized the moment and deservedly went through thanks to a goal 10 minutes from time from substitute Paris Lock.
The Clarets had reached the quarter-finals last year before losing to eventual winners Manchester City.
But on the club’s first visit to the new Plough Lane, Tony Philliskirk’s youngsters never looked like launching another run.
The Clarets didn’t click all night and barely made a chance as they looked to make it a hat-trick of wins after back-to-back league victories in the northern group of the U18 Premier League.
And Lock’s late intervention confirmed Burnley’s exit as the Dons avenged their defeat from the clubs’ previous meeting in the competition in 2015.
Wimbledon – who play their football in the South-East Division of the EFL’s Youth Alliance – had knocked out Oxford United and AFC Sudbury to reach this stage before the competition had been mothballed.
And the League One club more than held their own in a competitive first half almost devoid of chances.
The one real sight of goal came the Dons’ way with nearly half an hour gone but from Troy Chiabi’s cross, Dylan Adjei-Hersey put his header too close to goalkeeper Sam Waller who was able to beat the ball away.
Burnley – missing a handful of likely starters and with half-a-dozen first-year scholars in their line-up – had their moments when widemen Finlay Armstrong and Dara Costelloe looked as though they might make something happen and Will Hugill did put one early effort just wide of the target.
But the visitors generally failed to impose themselves sufficiently on the tie which remained in the balance without an opening goal.
With extra-time a growing possibility the Clarets still hadn’t created a clear-cut opening but with 12 minutes to go they finally tested Dons’ young England keeper Matthew Cox.
Dylan Moonan’s fine through-ball released Michael Mellon who wasn’t helped by a diminishing angle but still got away a low shot which Cox saved low to his right.
But any suggestion that would give Burnley the initiative was soon dismissed as the Dons grabbed the winner as two of their substitutes combined.
Aron Sasu made the decisive burst into the penalty area and from his low cross, Lock slid in to squeeze the ball inside the far post.
And while this hardly reprised the shock of Wimbledon’s FA Cup win at Burnley 46 years ago – when they were still a non-league side – it was still a notable victory for the Londoners, who will now enjoy their local derby with Spurs.
Burnley: Waller; Williams (Hamilton 83), Sassi, Gallagher-Allison, Carson (Coppack 70); Costelloe, Hugill, Moonan (Ratchford 79), Armstrong; Unwin, Mullin. Substitutes: Casper, McCullough, Eastmond, Couch.
AFC Wimbledon: Cox; Mason, Ogundere, Sutcliffe, Hallard; Ali, Frimpong; Adjei-Hersey, Chiabi (Wallace-Ming 90), Bartley (Sasu 65), Yeboah (Lock 77). Substitutes: Bangura, Few, Jones, Williams.