Steven Defour played for 90 minutes to complete his re-habilitation as the Under-23s got back on track with a fourth home win of the season.
Daniel Agyei scored twice in five first-half minutes before a slice of luck earned Tinashe Chakwana a second-half winner.
And the other big plus was another run-out for Defour who played his first full game since returning from his lengthy injury absence.
The former Belgium international was back on first-team duty for last Tuesday night’s Carabao Cup defeat at Burton – playing for just over 70 minutes – and was an unused substitute at Cardiff on Sunday as the Clarets won away for the first in the Premier League this season.
And another outing as an over-age player in the Professional Development League should now have him nearer cherry ripe to play a potential role against Huddersfield Town at Turf Moor on Saturday should the extra midfield option be required.
Defour had helped secure a win over Bolton in his last under-23 appearance a fortnight ago before a defeat to Hull City a week ago checked the Clarets’ momentum.
But despite letting a two-goal lead slip before the break, the side under the temporary stewardship of Academy Manager Jon Pepper regained control to see off a Crewe side that had won two of its previous three games.
Dwight McNeil was also included in the Burnley ranks and played a big part in the Clarets’ early dominance.
His early free-kick was headed just wide by Olly Younger before the winger, a permanent fixture in the first-team squad, twice went close when cutting in off the right flank to go it alone.
The opening goal finally came after 24 minutes when left-back Anthony Glennon produced a perfect cross for Agyei to dive and head home.
And the Clarets quickly doubled their lead when Agyei struck again, this time showing his pace and power to burst into the box before steering a low shot past William Jaaskelainen.
With McNeil, Defour and Mace Goodridge dictating things, Crewe had offered little threat.
But the visitors were offered a route back into the game when defender Ed Cook headed an own-goal past Anders Lindegaard from Harry Pickering’s free-kick.
Encouraged by that, the Railwaymen then grabbed an equaliser seven minutes before half-time when Younger hauled down Pickering and Lewis Reilly converted from the penalty spot.
The Clarets recovered from that set-back to hold sway again in the second half but it took a slice of luck to earn them maximum points.
Goodridge was stopped in his tracks as the midfielder advanced into the box but an attempted clearance from Travis Johnson crashed into the shins of Chakwana and rebounded into the back of the net.
It was no more than the Clarets deserved but Chakwana’s attempt to add a more deliberate fourth goal was thwarted 15 minutes from time when Jaaskelainen – watched by his father Jussi, the former Bolton and West Ham goalkeeper – made a fine save to tip over a the striker’s crisply struck shot on the turn.
Burnley: Lindegaard, Cropper, Cook, Younger, Glennon, Bayode (Blair 64), Goodridge (Howarth 58), Defour, McNeil, Agyei (Trialist 78), Chakwana. Substitutes: McMahon, Clarke.
Crewe: Jaaskelainen, Johnson, Offord, Lundstram, Sass Davies (Onyeka 82), Raynes (Fenton 70), Heath, Pickering (Robbins 64), Reilly, Linton, Lynch. Substitutes: Odipe, Booth.
Referee: Lewis Smith