Barca appeared to have been pegged back by a dramatic Inaki Williams equaliser but it was disallowed for handball.
The decision allowed Xavi's side to hold out its host in the face of intense pressure.
The visitors had to weather a storm in the first half as well, making the most of their survival on the stroke of half-time when the in-form Raphinha struck.
HIGHLIGHTS: #AthleticBarça 0-1
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Barça win by another narrow margin 💪#LaLigaSantander | #LaLigaHighlights pic.twitter.com/cy5QHRgA1D
Williams' disallowed goal was then followed by more late chances for Athletic but Athletic's efforts amounted to nothing as Barca got one over former coach Ernesto Valverde.
The victory restored Barca's advantage over second-place Real Madrid to nine points.
