A spirited second half performance from City was not quite enough as they slipped to their first defeat in five games at Craven Cottage.
The Potters put their hosts under considerable pressure in the second period and created a handful of openings, but were unable to find that crucial equaliser that they deserved for their efforts.
They bombarded the home side in the second half with a number of set pieces, and despite there being not too many clear cut chances, they will feel slightly aggrieved at leaving the Capital without a point.
Substitute Erik Nevland gave the Cottagers a first half lead after a brisk counter attack. Liam Lawrence had Stoke's best chance of the first 45 minutes when he fired narrowly wide from distance.
Ryan Shawcross went close with two headers and Ricardo Fuller was unlucky not to nod his side level after the break but the home side hung on for all three points.
City boss Tony Pulis made three enforced changes to the side that beat Blackburn Rovers last Saturday.
Richard Cresswell replaced the injured James Beattie in attack. Whilst knocks to Danny Higginbotham and Andy Wilkinson meant Danny Pugh and Stephen Kelly (who was making his second start for the Potters) occupied the full back slots.
On the substitutes bench, Carl Dickinson had his first inclusion since returning from his loan spell at Leeds United. Leon Cort, and Michael Tonge also returned to the matchday squad.
After their 0-0 stalemate with Middlesbrough last weekend, the hosts made only one change. An injury to Welsh international Simon Davies meant that he was replaced by former West Brom midfielder Zoltan Gera.
The visitors applied immediate pressure from the kick off and won a corner inside a minute thanks to good pressure by Pugh. Lawrence swung the ball over and it was then headed out as far as Rory Delap. Unfortunately his left foot volley flew over the bar to the enjoyment of the home support. Ricardo Fuller fired over from the edge of the box only moments later.
Fulham began to get a foothold on the game and the Potters were defending solidly in the opening ten minutes. Delap had another chance to give City the lead slightly against the run of play after nine minutes. He cut inside after a neat pass by Matty Etherington but again fired over from the edge of the box.
The hosts were forced into an early change when Bobby Zamora was replaced by former Manchester United striker Erik Nevland after 20 minutes.
For all their pressure, Fulham had to wait nearly 25 minutes for their first effort on goal. The ball dropped to Clint Dempsey on the edge of the box, but the American international's effort was never in danger of finding the net as it flew wide.
The hosts were in front just inside the half hour mark thanks to substitute Nevland. A Delap throw was cut out and Fulham broke with pace. Andy Johnson received the ball on the right hand side of the box and his low drilled cross was met by the Norwegian at the near post, who slotted coolly into the far corner.
Another substitution for the host due to injury saw Johnson replaced by another former Baggie Diomansy Kamara after 35 minutes. A minute later, Liam Lawrence flashed a shot narrowly wide from distance.
As the clock ticked into 39 minutes, Lawrence was somewhat harshly booked for what at first looked like a good challenge. Fulham surprised the visitors' wall with a short free kick and Paul Konchesky's low centre was almost turned in by Dickson Etuhu. Only a minute later, Konchesky fired over from close range after another surge into the City penalty area.
The Potters were under the cosh for the final few minutes of the first half, with Nevland heading high and wide. The Norwegian was booked soon after for a late lunge on Thomas Sorensen following a back pass from Faye. That turned out to be the last action of the first half and City left the field with plenty to think about for the second half.
The second period began in a similar fashion with the pressure being applied by the home side. A Dempsey shot was deflected wide and the visitors dealt with the corner. Danny Pugh was then treated for a facial injury after he was clattered into by Nevland.
Fulham came close again when Gera had a shot deflected wide from a corner after 55 minutes before Shawcross was booked two minutes later for a late tackle on Kamara.
The Potters were beginning to put a bit more pressure on their hosts with a number of dangerous throw-ins and corners. Shawcross came close with a header in the 69th minute following a corner from Lawrence, but his effort bounced over the cross bar. Fuller fired over just a minute later after he was played into space by Delap.
Stoke came close again when a Fuller header flashed wide from a corner in the 77th minute. The Jamaican then came close to heading home but Schwarzer plucked the ball out of the air at the vital moment, resulting in a foul on the 'keeper.
It wasn't until the 83rd minute that Tony Pulis made his first substitutions. Kelly was replaced by Ibrahima Sonko and Henri Camara replaced Cresswell to make his second appearance for City.
Pulis' side never looked like giving up, and came close again on the counter attack when Camara's cross was headed over by Shawcross after a sudden burst forward by the centre back.
Only three minutes later, Pugh landed awkwardly and left the field to be replaced by Dickinson. Dempsey then shot straight at Sorensen in what was Fulham's only real sight of goal in the second half.
The Potters continued to lay siege on the Cottagers' penalty area but were unable to force their way past a stubborn defence and left London without the point they perhaps deserved.
