Etherington latched on to Ricardo Fuller's cross seven minutes from time to inflict a fifth home defeat of the season on Fulham and move Tony Pulis' side up to 10th with their fourth win and 20th away point of the campaign, the same as Liverpool.
Stoke goalkeeper Asmir Begovic had to react quickly to deny Clint Dempsey in the second half but Fulham otherwise lacked any killer instinct despite Roy Hodgson recalling Brede Hangeland, Zoltan Gera, Danny Murphy, Damien Duff, Aaron Hughes and Dickson Etuhu to a strong side for their final home game of the season.
Pulis opted to stick with the same team that drew 0-0 with Everton on Sunday.
With the Europa League final just seven days away, many had predicted that Hodgson would put out a second string for the club's 61st game of a long season.
But aside from the injured Bobby Zamora, the side which Hodgson selected was so strong that he may well field the same team against Atletico Madrid next week.
Mark Schwarzer came out to punch Rory Delap's first trademark long throw in the fifth minute before Etuhu needed two minutes to recover after being hacked down by a mis-timed sliding tackle from Mamady Sidibe.
Wasteful passing from Fulham and resolute defending from Hangeland ensured neither goalkeeper was tested in the first 15 minutes.
Duff then found Gera in space in the 19th minute but he scooped his shot over from 10 yards.
Hangeland was barged into the advertising boards by Fuller as he shepherded the ball out but referee Peter Walton waved play on.
As a dull game limped past the half hour, the Stoke fans decided to entertain themselves with a conga around the Putney end stand.
Both sides failed to create chances but the game was given a little life when referee Walton had to stop play to talk to Dempsey, who argued with Ryan Shawcross after his path was blocked by the defender.
The first shot on target of the game came seven minutes from the break when Dempsey slipped in Gera who shot straight at Stoke stopper Begovic.
Fuller ranted at Walton after he failed to give a foul when Etuhu pulled him back just before the break.
Robert Huth then entered the book for arguing with the referee before Glenn Whelan fired harmlessly wide on the stroke of half-time.
Duff, who finished the first half clutching his leg, failed to emerge after the break and was substituted by Erik Nevland, who was making his last home appearance for the club before moving to Viking Stavanger.
Fuller beat his marker to send a glancing header wide from a Delap throw as Stoke looked for a quick goal after the break.
Hodgson came out of his dugout to vent his frustration at his side, who were struggling to get into their rhythm.
Shawcross was booked for a blatant tug of Dempsey's shirt eight minutes into the second half.
Etherington beat John Pantsil for pace down the left but his teasing cross flew across the box without a vital tap-in.
Etuhu's 15-yard header flew over just after the hour but Stoke continued to control most of the play.
Fulham hit back though through Gera, who picked out Dempsey at the back post but the striker's shot inside the six-yard box was tipped wide by Begovic.
Pulis looked for inspiration from Tuncay, who came on for Sidibe with 20 minutes left.
Etuhu climbed well to beat Delap from a Murphy corner but Begovic was equal to the midfielder's header.
Pantsil's ambitious 30-yard drive cleared Begovic's bar with just over 10 minutes left as Fulham regained control of the game.
But with little over seven minutes left the Potters took the lead when Fuller's cross skimmed off Tuncay's back to fall to Etherington who smashed his finish home off the Fulham woodwork.
Hodgson replaced Pantsil with striker Stefano Okaka as he looked to find a leveller while Etherington left the field for Salif Diao for Stoke.
A late challenge on Tuncay earned Aaron Hughes a booking towards the death as Stoke continued to frustrate the hosts in their search for an equaliser.
The home fans urged their team on but they could not find their way through a solid Stoke back line.
The Cottagers' attentions now turn to Arsenal before next week's Europa League final in Hamburg, where they will have to improve dramatically if they are to pick up their first major trophy in their 131-year history.