Substitute Jonatan Johansson netted a late winner to reward Norwich for a greatly improved second-half performance.
The Canaries were dreadful in the opening period when they created next to nothing, but raised their game considerably after the break and probably deserved the three points for the number of chances they carved out.
Stoke strikers Sammy Bangoura and Paul Gallagher had the best opportunities in a disappointing first half but neither side ever really looked like scoring.
Guinea international Bangoura got his head to a Luke Chadwick cross in the 11th minute but his effort did not unduly trouble England squad goalkeeper Robert Green.
Seven minutes later, Gallagher, on loan from Blackburn, volleyed over the crossbar when in a good position.
Leon McKenzie was making his first start since the Canaries lost the reverse fixture 3-1 in August, but while he appeared keen to justify his inclusion, neither he nor tricky team-mates Rob Earnshaw and Darren Huckerby had any significant impact.
Instead it was Norwich old boy Darel Russell who impressed, the Stoke midfielder drawing a couple of comfortable saves from Green with long-range shots, while Josip Skoko, on loan from Wigan, fired wide.
Paul McVeigh was the most lively player for the home side but missed the target with two strikes from outside the penalty area as a lacklustre half drew to a close.
But Norwich reappeared for the second period with much more purpose and after Earnshaw had made his first notable contribution, volleying wide, McKenzie gave them the lead in the 52nd minute, drilling home an angled shot.
The lead lasted for only six minutes though as Gallagher superbly converted a free-kick for his 10th goal of the season after Bangoura had been fouled by Gary Doherty.
Huckerby and Earnshaw almost combined to put Nigel Worthington's side back in front after 65 minutes. The former Manchester City wide man curled a lovely shot that goalkeeper Steve Simonsen could only parry and Earnshaw put the rebound wide.
Norwich looked a completely different side to that which had struggled through the first half and Doherty mishit a shot when connecting with a Huckerby cross before McVeigh forced another Parry from Simonsen.
Bangoura tested Green with a header in a rare Stoke attack.
But the Norwich pressure paid off in the 89th minute when Johansson, only on the pitch for three minutes after replacing McKenzie, tapped the ball home after being played in by McVeigh to clinch the last-gasp victory.
Teams:
Norwich Green, Fleming, Shackell, Doherty, Charlton, McVeigh,Robinson, Hughes (Etuhu 85), Earnshaw, McKenzie (Johansson 86),Huckerby.
Subs Not Used: Gallacher, Henderson, Colin.
Goals: McKenzie 52, Johansson 89.
Stoke Simonsen, Buxton, Hill, Duberry, Broomes, Russell,Mbuyi, Chadwick, Gallagher (Sweeney 80), Skoko, Bangoura.
Subs Not Used: de Goey, Kopteff, Wilkinson, Rooney.
Booked: Broomes, Buxton.
Goals: Gallagher 58.
Att: 24,223
Ref: P Crossley (Kent).