The Republic of Ireland internationals' strikes saw all three points handed to the home side in a game that was poor on the eye and devoid of any real quality
After a dire first half, Walters first tapped in from three-yards out after he converted a cross-shot from Matthew Etherington and in a final 10 minutes to forget for the travelling support, Rory Delap was then allowed to head in unopposed to secure the three points for the hosts.
For Stoke, manager Tony Pulis made two changes to the side that slipped to a 2-0 defeat at Swansea City. Winger Etherington recovered from a dead leg and replaced Dean Whitehead, while Matthew Upson came in at centre-back for Jonathan Woodgate.
Fulham boss Martin Jol replaced Zdenek Grygera with Aaron Hughes after the latter shook off the groin strain that kept him out of the 6-0 demolition job against Queens Park Rangers. Philippe Senderos, Kerim Frei and Bryan Ruiz all missed out due to injury.
The crispness of the autumnal weather at the Britannia wasn't reflected in the passing on the pitch in a desperate opening period. The lack of class was reflected in the 21st minute when Peter Crouch poorly scuffed a volley wide when unmarked from 10 yards out after Jermaine Pennant's cross evaded the leap of Hughes.
The next chance that came the summer signing's way followed a Marc Wilson free-kick on the edge of the area in the 28th minute. The ex-Portsmouth man's agricultural piledriver cannoned off the wall into Crouch's path close to goal, but some sharp scrambled defending saw the ball cleared for a corner.
Fulham had threatened even less than the hosts until the 40th minute when a delicate header from Bobby Zamora just looped to the right of the goal with Asmir Begovic well beaten.
A move of Premier League class finally appeared in injury-time when Pennant - the most dangerous player in the pitch - zipped inside Clint Dempsey and played a one-two with Crouch. An excellent first touch and drop of the shoulder got him clear through, but his composure deserted him at the death and he could only shoot agonisingly wide from right side of the six-yard box.
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The second half continued in the same bitty fashion as the team talk from both managers didn't seem to stretch to keeping the ball on the floor.
It took until past the hour mark for the first chance to be registered. In a hall mark of the game as a whole, a trademark Delap throw in caused chaos in the 64th minute.
With heart in mouth, goalkeeper Mark Schwarzer first meekly pushed the ball into Etherington's path on the far side of the six-yard box. The winger headed across goal, and the Australian was first caught under the ball by Crouch, before he somehow scrambled back to scrape the ball away from his goal line.
Stoke began to turn the screw and Delap then hit the post three minutes later, his cute turn inside Dempsey on the edge of the box leading to a shot that deflected off Steve Sidwell and on to the woodwork.
With momentum now with the visitors, Danny Murphy had to be at his sharpest to clear a Wilson header off the line from a corner.
The tide was now well in the home side's favour favour and the Stoke pressure finally told with a goal in the 80th minute from Walters. The striker showed his predatory instinct to slot home a skewed shot from Etherington after Fulham failed to clear a corner.
Stoke continued to push and were rewarded with a second goal through Delap in the 87th minute. The centre-midfielder brushed past the non-existent challenge from Riise to nod in Etherington's free-kick from the left flank.