A fit and firing Lewis Richardson made a welcome return to the goal trail as the Clarets continued their unbeaten start to the season.
The young striker had been forced to withdraw from England Under-17 duty through injury.
But a week on he was fit enough to claim his second goal of the season and help secure a point which could have been three but for a missed penalty from Rob Harker 20 minutes from the end at the DW Stadium.
A spurned spot-kick in injury time had also cost Burnley dear against league leaders Nottingham Forest in a dominant performance at Turf Moor last month.
But this time the Clarets should have been happier with a share of the spoils as they drew for the sixth time in nine league games to move up to second place in the U23 Professional Development League.
Wigan, who had won three of their last four games in a decent run of form, had chances of their own to add to Ali Koiki’s unfortunate own-goal which cancelled out Richardson’s early strike.
But the Clarets - unbeaten now in 11 league and cup games - will still feel they missed a trick as their late pressure failed to pay off after again surrendering a lead.
The visitors had made the ideal start with an opening goal after just five minutes.
Josh Benson – starting in a wide position – popped up in the penalty area to collect a pass from Ne-Jai Tucker and chip the ball across for Richardson to score with a smart volley on the turn to claim his first goal since the end of August.
Richardson carried a threat in and around the penalty area when he was able to avert some close attention from the Latics’ defenders.
But the Clarets couldn’t work another clear opening in a lively opening half, Harker going closest with an attempted flick at the near post from Ryan Cooney’s excellent ball in.
And Wigan were deservedly level at half-time – even if their equalising goal carried a large slice of good fortune.
On-loan Wolves winger Bright Enobakhare lived up to his name and in tandem with Charlie Jolley caused the Burnley back line – still missing the injured duo of Bobby Thomas and Ollie Younger – plenty of problems.
And when Enobakhare, who boasts almost 50 first-team appearances for Wolves, gave Adam Phillips the slip, his through-ball presnted Jolley with a clear run on goal.
Clarets keeper Lukas Jensen spread himself well to make a fine save but was left frustrated as the loose ball bounced off the legs of retreating defender Ali and into his own net to make it 1-1.
Jensen was becoming a central figure as the big Dane denied Enobakhar either side of the break to continue the positive impression he has made since signing last month.
And the goalkeeper's efforts should have paved the way for Burnley to regain the lead 12 minutes into the second half.
Jensen’s long kick was flicked on by Harker and when Richardson got goalside of Emeka Obi, the Wigan defender bundled the teenager to the ground.
Harker took on the responsibilty after Koiki's scoring run had been ended with his unsuccessful attempt against Forest, but fared no better as he saw his penalty saved by Dan Gyollai as he dived to his left.
Harker looked to make amends with a volley Gyollai did well to turn around the post 15 minutes later after a Phillips' ball had been diverted into his path.
And Burnley finished on top, pressing to the end for a winner as Richardson saw an effort blocked and Phillips twice couldn't convert from free-kicks earned by Richardson on a bruising night for the 16-year-old goalscorer, whose country's loss was the Clarets' gain.
Wigan: Gyollai; Golden, Obi, Long, Finley; Crankshaw, McGuffie (Perry 59), Merrie, Enobakhare (Baningime 82); Piggott, Jolley. Substitutes: Aspinall, Sanders, Galvin.
Burnley: Jensen; Cooney, Wilson, Glennon, Koiki; Tucker, N’Guessan, Phillips, Benson (Bayode 76); Harker, Richardson. Substitutes: McMahon, Cropper, Perkins, Harris.
Referee: Richard Holmes