Salif Diao's injury-time winner struck a devastating blow to Portsmouth's hopes of emerging from their crisis still with their Premier League status.
Pompey, facing a winding-up order and a possible nine-point deduction, remain eight points adrift of safety.
Frederic Piquionne tapped in to put Pompey in front but Robert Huth equalised with a free header.
Stoke had Andy Wilkinson sent off but Diao compounded Pompey's woes when he tucked in from Ricardo Fuller's pass.
The result is hugely damaging to Pompey's chances of avoiding relegation - they are rooted to the bottom of the table with only 12 matches to play.
But a more significant result could come after 1 March, when they will contest a winding-up order.
Should they lose the case in court and go into administration, they will automatically lose nine points.
Grant glum after last-minute defeat
And that may make this defeat seem irrelevant as relegation would appear almost certain - and the club could even become extinct.
But the loss is another heartbreaking episode in a chapter of Pompey's history that is already horrific.
Yet judging by this display on the pitch, it is clear the club's players - who have regularly had to wait for their wages - will continue to fight as hard as possible.
And that is despite five of the starting line-up against Stoke being on-loan players.
Nor was there any doubting the loyalty of the home side's supporters, who were in fine voice throughout.
After overcoming the initial nervy 15 minutes, where Stoke delivered countless crosses and Rory Delap throw-ins, Pompey look determined to record what would have been only their fifth victory of the season.
Portsmouth's Jamie O'Hara showed quality in midfield, while Quincy Owusu-Abeyie's pace and direct running gave them some attacking edge.
Pompey were unlucky not to take the lead when Piquionne applied to a superb finishing touch to Owusu-Abeyie's pass but the goal was harshly ruled out for offside.
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