Ten-man Stoke lost their unbeaten Europa League record and had to settle for second place in Group E as Besiktas came from behind to triumph 3-1 in Istanbul.
With the Potters having already qualified for the last 32, boss Tony Pulis left all 11 players who started against Tottenham last weekend at home but then saw his side take an unlikely 29th-minute lead through Ricardo Fuller.
Asmir Begovic had been superb in keeping Besiktas at bay but in the 59th minute Manuel Fernandes equalised from the penalty spot after Matthew Upson was sent off for felling Hugo Almeida, and goals from substitutes Mustafa Pektemek and Edu secured the points.
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