Burnley stretched their unbeaten run to four matches as they continue to put a disastrous start to the season behind them.
Having been twice denied by the woodwork, the Clarets had to show great resilience to fight their way back having gone behind.
In the end Burnley were full value for their first great win as they climb out of the relegation zone.
An action-packed game deserved more goals but some poor finishing stopped both teams from making the most of their efforts.
In the first half Burnley striker Robbie Blake fired a shot against the woodwork while at the other end Burnley keeper Marlon Beresford made two good saves.
The game really burst into life in the second half as both sides went all out for victory.
Beresford made two more stunning saves to shut out Tommy Mooney, while at the other end Gareth Taylor headed against a post.
The goal the game deserved finally arrived in the 74th minute when Jurgen Vanduerzen broke down the left and fired in a deep cross for Bjarni Gudjonsson to tap in at the far post.
Stoke were ahead for less than a minute before Arthur Gnohere headed home an Alan Moore cross.
Burnley continued to press forward and got the winner with eight minutes to go when Glen Little fired in a right-wing cross for substitute Dimitri Papadopoulos to glance home his third goal in two games.
Stoke pressed hard for an equaliser but were stopped in their tracks in the 85th minute when Mooney was sent off for serious foul-play following an off-the-ball incident with Tony Grant