Ritchie de Laet had scored against his old club to put the Canaries in front at the break.
After Jon Walters saw his penalty saved following Leon Barnett's red card on the hour, it looked as if Norwich would hold on - only for Stoke's pressure eventually to tell with Jones heading home to cap a fine Potters move.
Carrow Road last hosted top-flight football in May 2005, when Nigel Worthington's men failed to make their stay more than a flying visit.
Despite the partisan atmosphere in the 27,000-strong crowd, it was Stoke - coming on the back of their midweek Europa League tie, who made the early running, as Walters got in on the overlap to fire an angled shot at John Ruddy.
Anthony Pilkington - one of half a dozen changes by Canaries boss Paul Lambert from the side which drew 1-1 at Wigan - shaped to shoot from 25 yards, but could only blast the ball straight at Robert Huth.
Canaries captain Grant Holt was coming in for some rough treatment from the Stoke backline, who continued to give away needless fouls.
After 20 minutes, Elliott Bennett, a £1million signing from Brighton, got clear down the right, but his chip through the six-yard box was headed clear.
Holt nodded Naughton's sweeping crossfield ball to the far post back into the path of Pilkington, and only a flying block from Huth stopped the winger from firing Norwich ahead.
Stoke countered quickly after 28 minutes, working the ball out to Matthew Etherington on the left, who cut inside Barnett and fired an angled drive which Ruddy beat away.
The visitors were forced into a change on the half-hour when Jermaine Pennant, struggling with what looked like a calf problem, was replaced by Danny Pugh.
Jonathan Woodgate went into the book after 36 minutes for upending Bennett out on the far touchline.
From the resulting free-kick Norwich took the lead when former Stoke defender De Laet, on loan from Manchester United, glanced Bradley Johnson's curling delivery into the far corner.
The visitors were rattled, with Woodgate almost diverting a low cross into his own net which Asmir Begovic pushed around the post.
Norwich striker Chris Martin got the wrong side of Woodgate and into the Stoke box, but lacked support as eventually the danger was cleared.
Stoke emerged with some purpose for the start of the second half, with Walters drilling wide from a tight angle after breaking into the right side of the Norwich box.
At the other end, Martin - making a first appearance since February - saw his 20-yard drive pushed away by Begovic.
After 57 minutes, Holt was penalised for pushing over Glenn Whelan to concede a free-kick in a dangerous central position, some 25 yards out. Etherington beat the wall, but Ruddy flicked the ball over the crossbar.
Disaster struck for the home side on 63 minutes when Walters got ahead of Barnett and into the Norwich box, before tumbling.
Referee Neil Swarbrick ruled Barnett the last man, awarding a penalty and then sending the Norwich defender off. Walters took the spot-kick himself, but Ruddy guessed correctly to make a fine save - as the Carrow Road faithful erupted.
After 65 minutes, Lambert made a tactical change, replacing lively winger Pilkington with Daniel Ayala, who joined from Liverpool earlier this week.
Stoke, though, continued to press, as Norwich defended too deep.
Ruddy had to tip away a swirling cross from Ryan Shotton, which looked like it might loop in, the corner then flying through the six-yard box.
Jones blasted over from close range, but the visitors' pressure finally told in the third minute of added time when the striker headed in Whelan's cross.