The Swans cannot finish top of the group after a home defeat.
Swansea City have to at least draw their final Europa League match with St Gallen in two weeks time after slipping up at home and losing to Valencia 0-1.
The Swans had beaten the Spaniards 0-3 in the reverse fixture on the opening day of the current campaign, but a first half goal from Daniel Parejo sealed their fate.
Substitute Alvaro Vasquez had a goal disallowed somewhat dubiously before the forward had a strike cleared off the line late on, although the Welsh club’s fate is still in their own hands.
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