Standard Liege defender Vojvoda found himself alone inside the penalty area at a corner kick in the 67th minute and drilled the ball into the net to give Kosovo the points as the Czechs paid for the failure to finish their chances.
The visitors had opened the scoring in the 16th minute after a nifty combination when RB Leipzig forward Patrik Schick swept home a pass from Jakub Jankto with his left foot.
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Kosovo -- who only became FIFA members in 2016 -- equalised four minutes later when Elbasan Rashani raced down the flank and squared for Vedat Muriqi who muscled past a defender and directed the ball beyond keeper Tomas Vaclik.
The win took Kosovo to provisional top spot in Group A with eight points from four games and left the Czechs level on six with second-placed England, who have only played twice but face bottom side Bulgaria later on Saturday at Wembley.
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