The Stoke winger latched on to Ricardo Fuller's cross to smash his drive past Mark Schwarzer to inflict Fulham's fifth home defeat of the season and move Tony Pulis' side up to 10th in the table.
Matt finish: Matthew Etherington scores the winner for Stoke
Stoke goalkeeper Asmir Begovic had to react quickly to deny Clint Dempsey in the second half but Fulham otherwise lacked any killer instinct in what was largely a dull match.
Fulham manager Roy Hodgson recalled Brede Hangeland, Zoltan Gera, Danny Murphy, Damien Duff, Aaron Hughes and Dickson Etuhu to a strong side for the Cottagers' 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.
Ful focus: Fulham's Clint Dempsey under pressure from Robert Huth
Fulham fans left furious over Europa League final ticket fiascoFulham join the likes of Millwall, Middlesbrough, Cardiff and Rochdale in Sportsmail's list of unlikely cup finalistsFULHAM FC