Robin van Persie came off the bench to inspire Arsenal to a fourth straight Premier League win at home.
Gervinho had seen his clinical first-half strike from Aaron Ramsey's pass cancelled out by a close-range goal from former Spurs striker Peter Crouch.
But Van Persie swooped just six minutes after coming on as a second-half substitute to convert Gervinho's cross.
The Dutchman added a third goal when he diverted a shot past Asmir Begovic after another Gervinho pass.
The win sees Arsenal leapfrog Stoke to go seventh in the Premier League table and maintain a winning sequence at Emirates Stadium that is now five games in all competitions.
It was somewhat harsh, though, on the visitors, who had defended with strength and in numbers and looked good value for a point - until the introduction of Van Persie.
By winning, Arsenal brought to an end a run of four consecutive defeats in games after Champions League matches. Stoke's third straight away Premier League defeat followed a strong win over Maccabi Tel-Aviv in the Europa League on Thursday.
Gervinho had already had a sight of goal when he drifted in behind the visiting defence after 15 minutes only for Begovic to collect the ball after he miscontrolled it with his chest.
But the Ivorian gave Stoke's keeper no chance midway through the half, collecting Ramsey's clever lofted pass and keeping a cool head to slot home his second goal in Arsenal colours.
The strike should have been the signal for the home side to get on the front foot but the opposite happened, with Stoke gaining more possession and being rewarded for their efforts with an equaliser.
Arsenal players protested about the free-kick awarded against Laurent Koscielny for a foul on Crouch but they failed to defend it properly, losing three 50-50s in their own box as the visitors restored parity.
The goal was the 18th Arsenal have conceded in the Premier League this season, meaning they have now conceded more in their first nine games than they did in the whole of the 1998-99 campaign.
First Ryan Shawcross peeled off at the back post to return the ball across goal, where it was flicked on by Matthew Upson to Jon Walters, who nodded it goalwards for Crouch to side-foot home from three yards.
Van Persie's made an almost instant impression after his introduction in the 66th minute, converting Gervinho's cross following his powerful run down the right wing.
The duo repeated the trick eight minutes from time, with Gervinho advancing down the left wing this time and firing a pass into Van Persie, with Begovic failing to keep out the Dutchman's shot.
The Gunners skipper, who has recently stalled over a new contract, has now scored eight of his side's 15 goals this season.
Arsenal manager Arsene Wenger:
"It was a gamble to play him (Van Persie) but he has a special quality. He can open teams up and maybe when he plays, the confidence of other players grows.
"He is a very intelligent player and his record is just incredible. He was on the edge, but we knew we would get 20 or 30 minutes out of him.
"We took over in the final quarter of the game and it was a deserved victory at the end of a tough week.
"There is still a lot to do but the crowd is behind the team, they stayed with us during a difficult spell, and the team is playing with a lot of spirit."
Stoke manager Tony Pulis:
"The second and third goals are disappointing because we don't like teams getting in behind us and they did that both times.
"I thought our lads were very good for an hour and we tired after that. The free-kick we scored from was something we have been working on and we executed it very well.
"But Arsenal have got players who cost £16m on the bench, and that's why they are where they are.
"We've had a lot of games already this season and we've shown a fantastic attitude in all of those games."