Rochdale, who needed victory to snatch the title and automatic promotion back to League Two from leaders York, thought they had done enough when Emmanuel Dieseruvwe headed them in front after 95 minutes. His goal sparked a pitch invasion by home supporters that delayed the restart.
Stones struck the equaliser in the 103rd minute with York's last kick of the season, forcing the ball over the line in a scramble in front of the net as York threw 10 players forward.
Delighted York fans chanted "We are going up!"
The goal was confirmed by goal-line technology after referee Will Finnie consulted his watch, sending York fans streaming onto the pitch.
"Everyone said it this season, 'York-time' and there's a real belief and togetherness in this group of players," York City boss Stuart Maynard told DAZN.
"The players are warriors. When (Rochdale) scored, our players came over to the bench and said there is one last chance in us. We've done that all year.
"We're one big family. I love all of them."
York finished as champions on 108 points, returning to the Football League after a 10-year absence, while Rochdale ended two points back on 106 and must seek promotion via the playoffs, where only one additional League Two place is available.
On Friday, York City and Rochdale issued a joint call for an overhaul of promotion rules ahead of the title-deciding clash on the final day of England's fifth-tier National League.
"I hope Rochdale go up," Maynard said on Saturday. "It's criminal in this league that teams can get over 100 points and not go up."
Both sides missed out in the playoffs last year, when York were runners-up only to see Oldham Athletic - who finished three places and 23 points behind them - win promotion.
"Both clubs (York and Rochdale) sit on over 100 points. One of us will have to fight once more in the National League Play-Offs," a joint statement said.
"However, we both strongly believe that this shouldn't have to be the case."
The 3UP campaign was launched in February 2025, with the 72 clubs across the National League's three-division system calling for a third promotion place into the English Football League.
