The visitors went ahead in the ninth minute when Austria captain David Alaba completely miscued a header in midfield and Seferovic nipped in to lob the ball home from 25 metres with goalkeeper Ramazan Ozcan stranded outside his area.
Alaba atoned four minutes later by slotting home the equaliser but Eintracht Frankfurt striker Seferovic replied eight minutes from halftime when he flicked Admir Mehmedi's dinked cross past Ozcan.
Austria, who had won their last five games and were unbeaten in seven, last lost to Brazil in a friendly in November last year.
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(Writing by Brian Homewood in Berne, editing by Ian Chadband)
