The U23s extended their unbeaten run to six games, after a dramatic 4-3 win over Nottingham Forest at the Tameside Stadium under new boss Steve Stone.
It was Stone's first game in charge of the side, after watching the youngsters last time out at Liverpool in the Premier League Cup.
Dan Agyei snatched a 97th minute winner from close range to secure another three points in the Professional Development League, as the Clarets briefly rose to top of the league.
Forest took the lead with just six minutes gone through striker Yassine En-Neyah.
However, the Clarets levelled things up just two minutes later through Dwight McNeil.
Stone's side then took the lead shortly after through Tinashe Chakwana.
And moments later, Burnley had a third through an own-goal.
Forest then pulled one back before the break, as Jake Taylor fired home.
Then with 63 minutes played, Alex Mighten snatched the equaliser from the spot for the visitors.
However, Stone's side were not stopping there and snatched the late winner in the last minute of stoppage time.
The away side got off to the best possible start, as En-Neyah stroked the ball into the far corner past Adam Bruce with just six minutes gone.
Just two minutes later the Clarets had their equaliser, as McNeil picked up the ball from 25 yards out and drilled an effort at goal which bounced off the post before rolling in.
Shortly after the hosts took the lead, as Chakwana took advantage of Anel Ahmedhodzic's error in defence, before coolly slotting home past Liam Bossin.
And it was Ahemhodzic inavertently involved in the third, as Bossin's save from Agyei's shot bounced off the centre-back.
However, Forest pulled one back before the break through Taylor, whose fierce strike found the top corner from just outside the box.
It very much settled down early on in the second-half, until En-Neyah's ambitious lob fizzed just wide of the post just after the hour mark.
And it was the visitors who did strike next, as Mighten slotted home the spot-kick to pull the scores level.
Chakwana was then replaced by Marley Blair with 20 minutes to go, after colliding with the Forest goalkeeper just outside the box.
And as both sides pushed for the late winner, it was the Clarets who snatched it.
With Chakwana's injury resulting in seven added minutes, the hosts left it until the last minute of added time to grab the winner, as Agyei poked home Bayode's shot on goal.
The win saw Burnley rise to top of the league before Bolton's 1-1 draw with Sheffield United later in the day took the defending champions back to the dop - a point clear of the in-form Clarets.
Burnley: Bruce, Clarke, Younger, Glennon, Koiki, Bayode, Howarth, Benson, McNeil, Agyei, Chakwana (Blair 70). Unused substitutes: McMahon, Cook, Conn-Clarke, Harker.
Forest: Bossin, Richardson, Preston, Taylor, Ahmedhodzic, Iacovitti (Wright 58), Lawrence-Gabriel, Fornah (Coveney 89), En-Neyah (Hayes 6'), Mighten, Ariyibi. Unused substitute: Wright, Stewart.