Stoke produced a performance of grit and determination to achieve a first league win over Liverpool for 26 years.
Ricardo Fuller poked home after his initial shot had been blocked in a pinball passage of play in the area.
Earlier, Fuller had been denied what appeared to be a clear penalty when he was pushed over by Maxi Rodriguez.
Stoke wrapped up the win over a poor Liverpool when Kenwyne Jones slotted in coolly, before Lucas was sent off late on to add to the visitor's misery.
The result launched Stoke up the table, out of the relegation zone and into into 10th place - leapfrogging Liverpool in the process. Ahead of the game Stoke boss Tony Pulis insisted he had said all he wanted to say about referees, having claimed earlier in the week that decisions were repeatedly going against his side.
But he might find it hard to completely move on after the Potters appeared to be denied at least one penalty in the first half - the clearest being when
Maxi knocked over Fuller. There were also incidents involving Martin Skrtel, who twice had his arms wrapped around Robert Huth.
However, Pulis will be delighted that it did not cost Stoke this time as they stuck to their task and deservedly beat a disjointed Liverpool side, whose six-match unbeaten run comes to an end.
Stoke were the better team, pressing high up the pitch and playing at a tempo that Liverpool found difficult to deal with.
The tried-and-tested approach of utilising long throws from Rory Delap caused chaos in the Liverpool box. One throw was eventually cleared to Dean
Whitehead, whose fierce drive brought a fine stop from Pepe Reina. From the resultant corner Kenwyne Jones directed a header wide.
Whitehead smashed a rising drive just over the bar shortly after before another Delap throw was headed on by Huth and almost hooked in by Pennant.
After 30 minutes of hustle, bustle and Stoke on top, Liverpool finally stirred.
Having previously been unable to accurately find any intended target from five yards, Liverpool then managed two decent shots from distance in quick succession.
Steven Gerrard's effort from 30 yards was pushed around the post by Begovic, who then dealt well with a low shot from Raul Meireles.
After half-an hour the hosts' pace dropped, and that suited Liverpool.
However, Jones would have been clean through but for a poor touch but the striker did recover enough to deliver a cross that a sliding Matthew Etherington almost get on the end of.
Liverpool's response was a Gerrard shot from 20 yards that went well wide.
In a match short on quality and controlled football, it was perhaps not surprising that when the opening goal came it was borne of a passage of play that saw the ball bounce around like a pinball.
Liverpool failed to clear the ball out of their area after numerous attempts and Fuller eventually stabbed the ball home after his initial toe-poke came back to him.
Stoke might have increased their advantage, but Delap's shot took a deflection and flew into the side netting and when Jones got the better of Skrtel, he fizzed a left-foot shot wide of the far post.
Having been on the back foot, Liverpool suddenly sprung forward and when Kuyt pulled the ball back to Maxi, the Argentine's low shot almost squeezed under Begovic who made the save by sitting on the ball.
It was rare moment of incisiveness from Liverpool, whose afternoon was better summed by Fernando Torres' attempted pass that was thumped high into touch.
The striker had come into the match looking to score for the third consecutive match but his form deserted him.
As Roy Hodgson's men misfired, stoke took full advantage and they sealed a back-to-back victory - following the midweek defeat of Birmingham that ended a run of five straight league defeats - when Jermaine Pennant found Jones and the striker slotted home.
Lucas was then sent off after picking up his second booking when he kicked out at Etherington.