Arsenal were on the verge of snapping City's 47-game unbeaten home run after Gabriel Magalhaes' first-half header had put the visitors 2-1 up at the Etihad Stadium on Sunday, one of several flashpoints in the highly-charged match.
But substitute Stones fired in from close range in the eighth minute of time added on to leave City still top of the table.
Arsenal's massive defensive effort resolve was finally broken after they had played the entire second half with 10 men following Leandro Trossard's controversial red card for kicking the ball away before the break.
City dominated with an extra man, but couldn't find a way through until Stones swept home.
City were defending an unbeaten home run dating back to a 2-1 loss to Brentford in November 2022, while Arsenal had been within moments of their first victory at City since 2015.
City and Arsenal players clash towards the end of their highly-charged draw. (AP PHOTO)
Erling Haaland fired City ahead in the ninth minute with his 100th goal for the club in 105 appearances when firing past Arsenal goalkeeper David Raya.
But the game turned when Rodri limped off in the 20th after appearing to hurt his right knee - a huge concern for City's title defence.
Arsenal levelled two minutes later through Riccardo Calafiori's dazzling, curling effort from outside the area, a goal that left City complaining furiously about a free-kick which they felt shouldn't have been allowed to be taken quickly.
Magalhaes then headed the visitors in front from a corner in the first minute of first-half stoppage time, having come close from an almost identical routine shortly before.
There was still time for another pivotal moment before the break when Trossard was sent off for a second yellow card after kicking the ball away, leaving Arsenal complaining bitterly amid the tindebox atmosphere.
The draw ended City's 100% winning record in the league season, but left the defending champions still a point ahead of second-place Liverpool and Aston Villa in third, with Arsenal two points off the leaders in fourth.
In the day's other top-flight game, Brighton manager Fabian Hurzeler and Nottingham Forest boss Nuno Espirito Santo were both sent off in a bad-tempered end to their teams' 2-2 draw.
The dismissals were triggered by Forest midfielder Morgan Gibbs-White being shown a second yellow card in the 83rd at Amex Stadium for a reckless challenge on Joao Pedro.
That sparked angry reactions on the sidelines, with Espirito Santo and Hurzeler both shown red by referee Robert Jones for what the Premier League described as "unacceptable technical area behaviour."
Forest had taken the lead through Chris Wood's penalty in the 13th minute, with Jack Hinshelwood and Danny Welbeck then giving Brighton a halftime lead with goals in the 42nd and 45th before Ramon Sosa got the 70th minute equaliser.
