Defender Tomas Kalas, fresh from helping Fulham win promotion to the English Premier League, scored the only goal of the game in the first half in Schwechat, just outside Vienna.
Gernot Rohr’s Super Eagles had already lost 2-1 to England at Wembley last weekend, while the Czechs — who failed to qualify for the World Cup — had lost 4-0 to Australia in their previous friendly outing.
Nigeria will face Argentina, Croatia and Iceland in a testing Group D in Russia, with their World Cup opener against Croatia in Kaliningrad on Saturday, June 16.
They will be based in Yessentuki, by the Caucasus Mountains in southern Russia.
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