The Gills only needed a point to seal the League Two championship and their 2-2 draw with AFC Wimbledon did just that, with the Kent club establishing a comfortable advantage inside 23 minutes thanks to Deon Burton's neat volley and a header from former Dons striker Danny Kedwell.
However, Jack Midson halved the deficit with 25 minutes remaining and Jonathan Meades slotted home a late equaliser for the relegation-threatened Dons.
But despite seeing his side squander a two-goal lead, it was enough to pop the champagne corks and delight Allen.
"It's been an amazing 10 months," he said.
"The players have kept going all the way through the season, and to be the manager on this special day is the highlight of my career.
"I've been known as a manager who keeps clubs up, so to be champions is unbelievable. It's a lottery win, a Christmas Day, a priceless moment.
"League One is average. There's some good teams, there are some big clubs coming down from the Championship, and they will be scared stiff of playing us at the start of next season because we're going to be so strong.
"We will be powerful, we are moving forward and we've got to challenge for promotion. I don't think I've been employed to be mid-table. What failure aims for the middle? Why not set ourselves a target to go higher and be better?
"You've got to give some credit to AFC Wimbledon. I knew they were going to fight to the end and 2-2, it was tricky, tense and scary for me. Thankfully we held on."