Jon Walters completed another 90 minutes on the comeback trail as the Clarets ended Crewe’s seven-match unbeaten run.
Walters played his second game as an over-age player in the Professional Development League since recovering from knee surgery in January.
And the striker finished on the winning side that to a first under-23s’ goal for trialist teenage defender Ed Cook.
Cook followed up a free-kick from the impressive Dwight McNeil to slot the ball home four minutes before the break.
Ed Cook celebrates the winning goal
And that proved enough to hand the Railwaymen a first defeat in eight games and earn the improving Clarets a fourth win in seven matches as they moved to within a point of Barnsley – with one game in hand – in their quest to get off the bottom of the northern group.
Michael Duff’s side, looking for back-to-back wins at Turf Moor, started brightly with play-maker O’Neil testing William Jaaskelainen with a shot on the turn which the Crewe keeper turned around the post.
The visitors, with a handful of young players with League Two experience behind them, then dominated for a spell with some impressive football.
Jon Walters made his first Turf Moor appearance since August
But the nearest they came to opening the scoring was a curling effort from Oliver Finney which went just over the bar.
And after Walters had been denied by Jaaskelainen after dis-possessing defender Brad Walker it was Clarets who grabbed the winner.
McNeil’s curling free-kick was parried by Jaaskelainen – the son of former Bolton, West Ham and Wigan keeper Jussi – but Cook reacted smartly to rifle a left-foot shot into the roof of the net in his first start at this level.
Crewe looked to hit back after the break and went close to an equaliser when Lewis Reilly, who scored twice for the senior side in a Football League Trophy tie earlier this season, shot against the far post from Alex Hurst’s low cross before Cook and Ollie Younger combined to block the follow-up from Tom Lowery.
Dwight McNeil was the Clarets' creative force
Luke Walsh, a real handful with his close control and elusive running with the ball, then curled a shot wide.
And after Brad Jackson had been denied by Jaaskelainen at the other end from a chance to make the points safe, it took a fine finger-tip save from Conor Mitchell to keep out a shot on the turn from Walsh to secure the Clarets’ seventh win of the campaign.
Ollie Younger helped keep a clean sheet a day after signing a new deal
Burnley: Mitchell, Birch, Cook, Younger, Koiki, Bayode (Chakwana HT), N’Guessan, McNeil, Jackson, Walters, Fleming (Goodridge 57). Substitutes: Stone, Perkins, Massanka.
Crewe: Jaaskelainen, Johnson, Adebisi, Griffiths, Lundstram, Walker, Lowery (Heath 74), Finney, Reilly, Walsh, Hurst. Substitutes: Sass-Davies, Appleyard, Barlow, Johnson.
Referee: Einar Ingi Johannsson