The winger scored close-range goals in the 13th and 43rd minutes before Stoke repelled a fierce onslaught in the second half to dent third-place Spurs' title challenge.
Emmanuel Adebayor halved the deficit in the 62nd minute with his eighth goal of the season, converting a penalty after Glenn Whelan was harshly adjudged to have tripped Luka Modric, but the visitors squandered a series of chances to complete the comeback.
Tottenham, which had centre back Younes Kaboul red-carded in the 82nd for two second-half yellow cards, missed the chance to provisionally move to within four points of unbeaten leader Manchester City, which visits Chelsea on Monday.
"It was a great performance from us and we showed what we're all about," said Stoke striker Peter Crouch, who joined from Tottenham on transfer deadline day in August.
"Obviously they're going to come at you. They are a top-class side and we were under the cosh. Everyone was working as hard as they could and they weren't going to take that result away from us."
Stoke's second straight victory lifted the team to eighth place but it was fortunate to come away with a win after replays showed defender Ryan Shawcross clearly used his right arm to stop Kaboul's goalbound shot in the 74th. Moments later, Adebayor had a goal wrongly disallowed for offside.
Spurs' last visit to Stoke ended with their elimination from the League Cup at the third-round stage in September and 2½ months on, they couldn't cope with the hosts' high-intensity start.
"We just started sloppily," Tottenham manager Harry Redknapp said. "At halftime, we sorted things out ... and dominated them in the second half. We took control of the game."
Crouch caused Tottenham's defence all sorts of problems in the first half and played a crucial part in the build-up to Etherington's first goal.
Bringing down Ryan Shotton's steepling deflected cross - possibly with his right arm - Crouch shrugged off the challenge of William Gallas and attempted a close-range shot from an acute angle that was saved by Brad Friedel.
The ball fell into the path of Etherington, who swept into an empty net.
The left winger, who played for Spurs from 2000-03, made it 2-0 just before the break, meeting a flick-on from Jon Walters with a scuffed shot that bounced into the net from 8m out.
The second half was a different story, with Tottenham - bidding for a seventh straight victory - launching wave after wave of attacks after Adebayor made it 2-1.
Stoke goalkeeper Thomas Sorensen saved well from Parker and Adebayor, while substitute Jermain Defoe had a goalbound shot blocked.
Having been given a yellow card in the 67th minute for dissent, Kaboul was dismissed 15 minutes later for a clip on Walters, helping Stoke to close out the game.
