Tony Pulis' side were coasting after a rousing display in the opening 45minutes, but visiting substitute Clint Dempsey inspired a revival for Roy Hodgson's men.
Stoke were forced to make a late change after goalkeeper Thomas Sorensen damaged a finger in the warm-up and had to be replaced by Steve Simonsen.
But Pulis' team made a bright start in the freezing conditions as Matthew Etherington's sweet finish was ruled out for offside in the second minute.
Sanli Tuncay scored Stoke's first Premier League goal for almost five hours after the Turkey international won a right-wing corner in the 12th minute.
Robert Huth's header from Etherington's in-swinging delivery was going wide, but Tuncay was lurking at the far post to nod past Mark Schwarzer from a yard out.
Fulham won a couple of corners in rapid succession as they attempted to hit back, but Stoke were hungrier for battle as Mamady Sidibe fired straight at Schwarzer from the busy Etherington's pass.
Stoke, again roared on by a passionate home support, were denying the visitors room to manoeuvre as they chased and harried for every ball.
And it was no surprise when Pulis' fired up troops capitalised after Paul Konchesky's crude foul on Liam Lawrence in the 34th minute.
Etherington bent his delivery towards the far post and the ball sailed straight through for Abdoulaye Diagne-Faye to slide in his shot from point blank range at the far post.
Stoke were in dreamland three minutes later when Sidibe fired their third on the turn after Tuncay, Etherington and Danny Higginbotham had left the Fulham defence mesmerised.
Tuncay received rapturous applause when he limped off with a knee injury in the 42nd minute, but his replacement Ricardo Fuller went close on three occasions before half-time.
The Jamaica star had two attempts cleared off the line in the mayhem caused by another Etherington corner before a third effort by Ryan Shawcross was charged down.
Fulham's towering defender Brede Hangeland, who passed a late fitness test, was replaced by Chris Smalling at half-time.
And Bobby Zamora, who injured his arm in a tangle with Faye which rightly earned the Stoke skipper a booking, soon followed as Dempsey entered the fray.
Dempsey quickly made an impression as his pass to Damien Duff led to the visitors reducing the arrears in the 61st minute.
Duff struck a venomous left-foot shot after cutting in from the right and the ball took a deflection off Shawcross to leave Simonsen without a hope.
There were no further scares for Stoke, who almost restored their three-goal cushion when Fuller skinned Konchesky only to be denied by Schwarzer, before Dempsey scored a stunner five minutes from time.
Fellow substitute Erik Nevland headed on a punt forward by Stephen Kelly and Dempsey struck a fantastic half-volley from 25 yards which soared into the roof of Simonsen's net.
But Stoke certainly deserved the three points on the overall balance of play and they came through a tense finale without further damage.