The Potters had not lost at the Britannia Stadium in the league since last February but Walters headed into his own net in first-half injury time and remarkably repeated the trick in the 62nd minute. Frank Lampard netted a penalty after Juan Mata went down and Eden Hazard rounded off the scoring with a long-range screamer.
Stoke were awarded a 90th-minute penalty but the luckless Walters could only find the top of the bar.
Kenwyne Jones came close to putting Stoke in front after his shot beat Petr Cech but rolled just wide.
Cech then saved from Steven Nzonzi but a break in the 25th minute provided Chelsea with a great chance as Demba Ba found Lampard running into the area, only for Asmir Begovic to save with his right leg.
But with injury time almost up, Cesar Azpilicueta swung in a cross which Mata was beaten to by a diving Walters, who powered the ball past his own keeper.
Stoke thought they had a penalty when Matthew Etherington fell under Azpilicueta's challenge but he had already been flagged offside. The killer goal arrived in the 62nd minute when from Mata's corner, Walters got ahead of Lampard but could only find his own net once more.
The Potters conceded a penalty three minutes later when Mata went down under contact from Huth as Shawcross also slid in. Lampard smashed the penalty down the middle before then shooting straight at Begovic from point-blank range.
The visitors got another in the 73rd minute, though, as Hazard's 30-yard drive rocketed into the top corner.
John Terry, on for a little over 10 minutes, conceded a penalty with a foul on Walters but there was no redemption for the striker.