Substitute Max Clayton scored with his first touch to earn Crewe victory over managerless Coventry.
In the second game between these sides in four days - following Wednesday's Johnstone's Paint Trophy northern final - Leon Clarke fired the hosts ahead.
But the Alex, aggregate winners of the final, drew level when Mark Ellis volleyed in Gregor Robertson's corner.
Robertson was then needed to clear Carl Baker's drive off the line, before Clayton lobbed keeper Joe Murphy.
The 18-year-old's sixth goal of the season moves Crewe just three points behind play-off chasing Coventry in 11th place.
It was only his second league strike of the campaign, almost six months on from scoring the only goal of the game in the Alex's 1-0 win over Coventry at Gresty Road back on 1 September.
VIEW FROM THE DRESSING ROOM
Coventry City caretaker manager Lee Carsley told BBC Coventry and Warwickshire:
"I thought we started the game well, we pressed and harried them, then we shot ourselves in the foot. From our view it's two goals we could have stopped, so it's disappointing.
"You sometimes don't mind seeing a good goal go in against you, but we gave those two away.
"I told them that there's no point in sitting in there feeling sorry for themselves. Tuesday [away at Bournemouth] is a massive game for us. I still believe they can do it, but it doesn't matter what I believe, it's down to them.
"Wednesday night took a lot out of them emotionally. When Crewe got their equaliser today I think a little bit of feeling sorry for themselves and feeling tired crept into it."