The Clarets got the point they needed to move to the top of the Professional Development League’s northern division.
A first-half goal from Jordan Cropper and a penalty save from Anders Lindegaard extended Burnley’s unbeaten run to nine games.
And ending Crewe’s six-game winning streak was enough to take the Clarets to the top of the table on goal difference – edging ahead of Leeds who they face at the Barnfield Training Centre next Tuesday.
Another youthful Clarets’ line-up went ahead when a cross from right-back Cropper (above) after 13 minutes was deflected into the net.
Midfielder Josh Benson almost doubled the lead with a long-range free-kick which clipped the top of the crossbar.
Crewe equalised with just over an hour gone when Travis Johnson picked out Oli Finney to fire home via the underside of the bar.
The Alex then had a chance to win it just three minutes later when Finney’s shot struck a hand in the penalty area.
But the Clarets’ keepers have made a habit of penalty saves in the under-23s this season.
And Lindegaard took his turn to step up by making a fine block to turn away Tommy Lowery’s attempt and keep Steve Stone’s men climbing.
Burnley: Lindegaard, Cropper, Glennon, Clarke (Cook 16), Koiki, Howarth, Benson, Taylor (Harker 70), Blair (Chakwana 50), Agyei, Bayode. Subs: McMahon, Thomas.