The 36-year-old striker twice hit the woodwork, among other wasted chances, but kept his cool to slot home a 75th-minute winner for the Catalan giants.
Teenage starlet Lamine Yamal put Barcelona ahead with a deflected effort but Oihan Sancet pulled Athletic level from the penalty spot before half-time.
Lewandowski’s strike earned Barcelona their second win from two league matches under new coach Hansi Flick.
The former Germany and Bayern Munich boss had hoped to utilise new arrival Dani Olmo but with Barcelona unable to register him because of their financial difficulties, the former RB Leipzig playmaker could only watch from the stands.
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