The hosts took the lead through a first-half penalty after an error of judgment by Jamie Carragher, who was caught out of position before bringing the forward down.
The striker was brought down in the box by Jamie Carragher after a tussle between the two and stepped up to slam home in the first half as the Reds' miserable winless run at the Britannia Stadium continued with a second successive defeat at the ground.
Liverpool had the first chance of the game as Luis Suarez capitalized on a high bouncing ball that swirled in the wind by pushing past Matthew Upson, but the Uruguayan's half volley took a deflection and flew out for a corner, from which the forward was unfortunate to see a whipped Charlie Adam corner skim off his chest and bobble wide at the far post.
The visitors dominated the early exchanges, but Stoke could have found itself ahead as a Matthew Etherington free kick was whipped across the six-yard box, where Ryan Shawcross, whose shirt was being firmly gripped by Skrtel, failed to get a telling connection.
And the hosts were to get a penalty not long after, as Carragher was caught out by a looping Jermaine Pennant ball which Walters chased, and the veteran center half foolishly wrapped an arm around his fellow Scouser's waist as they duked it out. Referee Mark Clattenburg had no hesitation in pointing to the spot despite both players pushing and shoving.
Up stepped Walters, who slammed home down the middle to give the Potters the lead.
But Stoke so nearly handed Liverpool an instant equalizer as a Jordan Henderson cross was disastrously tipped into the path of Suarez by Asmir Begovic, who was fortunate that Shawcross positioned himself in front of goal to fling himself at the striker's shot, forcing it wide.
The visitors came close again when Suarez, who had drifted out to the flank after losing a couple of battles in the center, exploited the extra space and rolled a pass across the box to Skrtel, who steamed into the box before unsurprisingly smashing over.
Suarez, at the hub of every Liverpool attack, fashioned a chance for himself as held off Shawcross before rolling around him, only to find the angle too narrow as Begovic comfortably collected his chance.
It was the last attempt of a frustrating half for the visitors, who had started brightly before being matched by their industrious opponents.
Neither manager made a change at the break, although Stewart Downing switched flanks with Henderson, with Robert Huth following the England winger to the opposite side of the pitch.
The second period started slowly, much unlike the first, but there was a flurry of chances on the 60-minute mark as Jose Enrique freed Henderson with a defense-splitting ball, but the youngster fired straight at Begovic and then again from the rebound, with the ball falling to Charlie Adam, who blasted into Upson's chest before dribbling into the box and seeing a close-range effort pushed wide by the Bosnian shot-stopper.
That flood of chances saw Huth replaced by specialist fullback Andy Wilkinson, and Kenwyne Jones came on for Etherington, while Dalglish threw on Andy Carroll and Craig Bellamy for Dirk Kuyt and Henderson, respectively. Wilson Palacios would soon come on for Rory Delap.
Liverpool's deadline day signing almost made an instant impact after tearing down the left and floating a cross to the back post, where Downing could only head straight at Begovic.
The visitors rained down on their opponents' box with some long balls as the heavens opened, but they struggled to disrupt Upson and Shawcross, who continued to frustrate Suarez on the ground, with the striker twisting and turning in the box to try and find space to shoot, only to be shepherded away by both defenders.
The livewire forward continued to be a menace and earned a corner with a driving run and shot, but could not beat Shawcross to a Downing cross into the area.
And the Uruguayan was unfortunate not to get a penalty late on when his reverse ball across the face of goal appeard to strike the arm of Upson.
Suarez was then gifted a golden chance to equalize in injury time when Begovic spilled an Adam cross straight into his path, but the 24-year-old lashed his effort wide of the post.
That frustration summed up Liverpool's afternoon, as the club had been continuously thwarted by a combination of Upson, Shawcross and Begovic, who all shined to keep up Stoke's unbeaten start to the season.