The Cod Army needed just a draw to condemn Blackpool and Doncaster to the fourth tier, with victory taking them to 51 points.
Bobby Grant struck in sweetly off the underside of the bar from more than 25 yards to put the hosts in front.
Fleetwood's Devante Cole then miscued from close range, but fired in shortly after from David Ball's cross-shot.
It was only a second win in 13 attempts for Steven Pressley's side, who finished 19th, five points clear of the relegation zone.
Despite being involved in a relegation scrap, Fleetwood have lost just six home league games this season - the same number as third-placed Walsall.
Crewe ended the campaign six points adrift at the bottom, without an away win since November.
Crewe manager Steve Davis told BBC Radio Stoke:
"It was a disappointing end to the season from us. The first half was nowhere near good enough.
"We didn't hold back afterwards. We let the players know how we feel about the season. We gave them ten barrels.
"They did not work hard enough and didn't show enough. We were not dangerous enough and we didn't close people down enough.
"We wanted to come here, make it difficult for them and try to upset the odds. We had a lot of possession, especially in the second half, but we didn't create enough."
Two early goals helped Fleetwood ease past already-relegated Crewe to secure their League One survival.