Etherington's decisive strike was virtually Stoke's only shot on target and a solitary moment of quality in an otherwise dour affair.
However, it is the potential loss of key midfielder Duff that may cause Fulham boss Roy Hodgson greater concern ahead the European showpiece in Hamburg in seven days' time, although there was nothing to indicate that the Irishman's substitution was anything more than precautionary.
Hodgson had insisted before kick-off that the Cottagers would not be distracted by their European adventure and he named his strongest possible side, with Dempsey playing up front in the continued absence of Bobby Zamora.
Stoke's previous visit to west London had resulted in a 7-0 hammering at Chelsea 10 days ago, so it was little surprise that Tony Pulis's side appeared focused on keeping it tight in defence this time around.
The chance to finish in 10th spot beckoned for the winner - a placing that would represent Stoke's best league finish since 1975 - but both sides appeared happy to settle for a point in the early stages.
The first half was a forgettable affair that delivered just one shot on target - a 20-yard drive from Zoltan Gera that flew straight into the arms of Asmir Begovic after 39 minutes.
The Hungarian was at the heart of the rare moments of excitement in the opening period. He fired narrowly over from Duff's cross and cleverly sent Dempsey through on goal before Robert Huth made a saving challenge.
Stoke began the second half in comparatively lively fashion and their first chance of the match arrived from a familiar source when Rory Delap's long throw was nodded inches wide by Fuller.
The scare roused Fulham into something approaching urgency and they almost took the lead midway through the second half, with Gera once again in the thick of the action.
The midfielder played a sublime reverse ball to Dempsey at the far post but the American's close-range volley was brilliantly kept out by Begovic.
Dempsey, keen to secure a spot in Hodgson's cup final line-up, then had two more good efforts from distance but both failed to trouble the keeper.
The game seemed to be petering out for a draw when a moment of magic from Etherington, named this week as the Potters' player of the season, sealed victory.
Fuller burst down the right-hand side and took advantage of a slip by Paul Konchesky to send a far-post cross to Etherington, who blasted the ball into the roof of the net to put the visitors on course for their best league finish for 35 years.
Fulham manager Roy Hodgson on his side's injury problems ahead of the Europa League final:
"We think one of Damien Duff's muscles was cramping up. That was a blow of course. We hope it's not too serious. I hope he'll be fit for the final. The medical staff don't think it's a muscle tear or anything like that.
"Bobby Zamora stands a chance of making it but he's not making vast amounts of progress on a daily basis so it could be touch and go.
"It's very disappointing to lose, especially seeing as the evidence showed it was handball which deflected the ball over for the goal."
Stoke manager Tony Pulis on his side beating last season's points total:
"We're only the second club to have beaten their points tally in their second season, so so much for second-season syndrome. That's a fantastic achievement for everyone at the club.
"We got beaten 7-0 at Chelsea two games ago and we have played a top team in Everton and we have won here tonight. We have had two clean sheets now so that shows our spirit of togetherness."
"Roy picked his best side tonight but we showed great resilience and spirit. I think it's been a great response from the players."
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