The Ghana youth international grabbed the match winner three minutes into the second half
It was Salzburg who scored first in the 10th minute through Brazilian Wamberto before Atanga provided the assist for Stefan Maierhofer to draw level after 25 minutes.
Atanga, on-loan, has now scored three goals in 12 league matches for the side he joined during the January transfer window.
He was replaced seven minutes from time by Barnabas Varga.
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