It was a case of unlucky thirteen for the Potters as Charlton Athletic inflicted defeat for the first time since November 10th.
Lloyd Sam's late header secured all three points for Alan Pardew's side, but Jon Parkin could have rescued a point for City after he burst through in the last minute.
City remain in fourth position in the Championship, four points ahead of seventh placed Cardiff City.
Tony Pulis opted to name an unchanged side ahead of the clash with Salif Diao retaining a place on the bench.
Charlton started the brighter of the two side's with new signing Andy Gray causing the City rearguard problems.
The former Burnley hit-man linked up well with former Potter Chris Iwelumo after just two minutes, but his shot was well blocked by Ryan Shawcross inside the 6-yard box.
Iwelumo almost headed the hosts in to a 17th minute lead following Matt Holland's in-swinging corner, but the powerful forward saw the ball blocked by Carl Dickinson.
Lloyd Sam was next to try his luck from range, but after firing through a crowded 18-yard box, Shawcross hooked the ball away from danger off the line.
The right winger went close again moments later, after his shot was deflected inches past Steve Simonsen's right hand post via the head of Leon Cort.
City first assault in to the Addicks penalty area came in the 22nd minute, with Ricardo Fuller almost producing a moment of brilliance.
The pacy Jamaican neatly controlled 30-yards out, swivelled and sent a curling effort just over Nicky Weaver's crossbar.
A trademark Rory Delap throw-in almost resulted in Charlton full back Kelly Youga heading in to his own net on the half hour.
City had to defend bravely as the first half wore on, with Patrick McCarthy heading against the post from four yards before Andy Griffin cleared the ball off the line and away from the fast approaching Gray.
A dangerous Liam Lawrence ball in to the penalty area almost found the un-marked Cort who swung his foot at the ball, but to no avail.
Darren Ambrose had the last effort of the half with a rasping thirty yard effort which flew well over.
City came out of the half time interval all guns blazing and some slick passing between Cresswell and Pugh released Fuller, who fired goal-wards only for Weaver to save with his outstretched left arm.
The hosts soon began to take the game to the Potters however, and a defensive mix up let in Chinese international Zheng Zhi, but his shot was well saved by Simonsen.
In the 55th minute Fuller used his power and pace to burst past Youga, and after taking a nice touch he fired a rasper towards goal but agonisingly it went just past the left hand post.
Simonsen reacted well to save from Ambrose, before Shawcross did just enough to put off Iwelumo who should have tapped the ball in to an empty net, but somehow missed.
Dickinson attempted a long range effort which dipped just over the bar in the 70th minute, before Charlton substitute Luke Varney went close with a header.
With the game looking more and more likely to end all square, the Addicks took the lead with just seven minutes remaining.
Former Crewe man Varney somehow missed with the goal at his mercy, but he recovered well to whip the ball in to Sam who headed the into the back of the net.
Substitute Jon Parkin almost earned the Potters a point in the 89th minute, but his shot was saved outstandingly by Weaver at the near post.
CHARLTON (4-4-2): Weaver; Moutaouakil, McCarthy, Bougherra, Youga; Sam (Semedo 86), Holland (c), Zheng, Ambrose (Thomas 71); Gray, Iwelumo (Varney 66). Subs: Randolph, Fortune.
CITY (4-4-2): Simonsen; Griffin, Cort, Shawcross, Dickinson (Parkin 86); Lawrence, Delap, Eustace (c), Pugh; Cresswell, Fuller. Subs: Hoult, Zakuani, Pulis, Diao.
