Youssef En-Nesyri opened the scoring for Malaga in the 13th minute, but Markel Susaeta netted the equaliser just four minutes later on Sunday, reports Efe.
Mikel San Jose scored the second goal for Athletic one minute before the end of the first half.
Last-place Malaga fought to score the equalizer, but forward En-Nesyri failed to convert a penalty kick in the 61st minute.
With just six minutes to go, En-Nesyri was sent off after he was shown a second yellow card.
With the home win, Athletic, which had two losses and four draws in the past six games, is in 12th place, with 31 points.
Unbeaten Barcelona leads La Liga with 65 points.
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