Second-half goals from Luke Murphy and Chuks Aneke ensured the Alex young guns ended the season in style.
Murphy's penalty opened the scoring before Aneke put the result beyond doubt with a superb finish four minutes from time.
Crewe started the game with a team of players who had gone through the club's famous youth system, but it was still an experienced line-up with more than 800 appearances between them and only goalkeeper Ben Garratt making his debut.
Davis said: "I'm immensely proud of all the boys. It's a massive achievement for this club.
"It was a brave decision and it could have backfired, but the lads showed how talented they are and what this club is all about.
"If it had gone wrong it could have fallen flat and everyone would have been gunning us down, saying their clubs could have sent out their kids to get beaten four or five nil.
"Dario Gradi has played more a part of his than anyone and he would have been a very proud man to see the result of all his hard work.
"We set ourselves a target of 50 points at the start of the season so we could never have imagine to have done as well as we have.
"But we are ambitious and we will build through the summer and see if we can push this club on even further."