It was the club's sixth promotion since being founded as an alternative to Wimbledon FC when the 1988 FA Cup winners announced plans to move 60 miles north to the city of Milton Keynes.
After two years of negotiations and controversy, the original team were renamed MK Dons in 2004.
Lyle Taylor scored after 78 minutes and substitute Adebayo Akinfenwa converted a penalty 11 minutes into added time at Wembley Stadium -- the venue of Wimbledon's FA Cup final win over Liverpool 28 years ago -- to beat Plymouth.
Wimbledon's triumph means they will next season face MK Dons, who were relegated from the Championship (second tier) after finishing second from bottom of the standings.
The teams have only met three times before in cup matches at Milton Keynes with AFC Wimbledon winning once.
FAIRYTALE TRIUMPH
AFC Wimbledon manager Neal Ardley, who spent most of his playing career at the south-west London club, was emotional after they secured a place in League One for the first time.
"To stand there in front of 25,000 people who 14 years ago had their club ripped away from them and have been through so much, to stand there as one of their own who has come through the ranks at the age of 11 -- you can write anything you want, it doesn't get any better than that," he said.
MK Dons, who retained the Wimbledon nickname 'Dons' when the team relocated, returned all the old replica trophies and other memorabilia in 2007 when they declared themselves a new club.
The 34-year-old Akinfenwa said after the match he was being released by the club but was philosophical about leaving on such a high.
"Come on now, there ain't no better way to send off. To see this team get promoted, to score with the last kick of the game, I couldn't even write that," he said. "I said let's complete this fairytale, and that's what we've done.
"I'm going to miss this team, I'm going to miss this place but there ain't no better way to leave it. It's about progression, and AFC Wimbledon are getting stronger and stronger. It's what dreams are made of, it's beautiful.
"I think I'm technically unemployed, so any managers hit me up on the WhatsApp and get me a job."
(Writing by Ken Ferris; Editing by Brian Homewood/Greg Stutchbury)
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