Malaga thought new boy Martin Demichelis had secured all three points in Andalusia, only for the Basque boys to be rescued by Martinez late on.
However it was just one goal each that settled this evening's fixture, Martin Demichelis who joined from Bayern Munich made himself a fans favorite with 80 minutes on the clock, flicking a header into the corner of the net, only for his thunder to be stolen by Javi Martinez in stoppage time.
Atheltic Bilbao began the game in a positive fashion, starlet Iker Munain drawing a foul from Antonio Apono. However, David Lopez's effort was well covered in the center of the goal by Malaga keeper Sergio Asenjo.
The visitors continued a useful spell of pressure with a series of corners but it was a corner for the hosts which almost made the crucial breakthrough, Salomon Rondon flashing a shot just wide of the left post.
Ander Iturraspe tested Asenjo once more just after ten minutes played, but again the Andalusian keeper collected comfortably.
Malaga were beginning to settle after a busy transfer period in the last week has put many players under pressure for a starting place, with all eager to impress it was Apono who looked dangerous going forward and perhaps should have given the home team the lead. The midfielder met a free-kick on the six-yard box but he couldn't get the ball on target for the Anchovies.
Apono again was given the time and opportunity to pull the trigger from distance, this time sailing a shot just over the bar with Gorka Iraizoz scrambling.
Los Leones themselves were desperate to start their post Christmas schedule with a bang, Javi Martinez twice bringing the San Mames faithful to their feet, if only to gasp as Bilbao struggled to maintain their early tempo.
The Basque club started the second-half brightly, causing confusion in the box for the hosts who had to resort to an up-and-under to clear their lines.
Ten minutes into the second period Fernando Llorente found himself in space twice, first sending a header just past the post and then two minutes after he got in front of his marker to latch on to a cross from the left, but was offside as he poked the ball at Asenjo.
Martin Demichelis on league debut, having joined from Bayern Munich, found his way into the book despite taking the ball, the Argentine international brought down Martinez on the break and the referee produced a yellow card.
After an hour played the game was running end to end but without any class or quality to pierce open either of the two defenses but with time ticking away it was Malaga who looked the most threatening in the final third.
Bilbao squandered a fantastic chance to at least test Asenjo from the edge of the box with 18 minutes remaining of normal time. It was Javi Martinez who showed great strength to hold off a challenge and spread the play wide right but once it came back to the midfielder he sliced the ball well high and wide.
Down the other end Apono was left wondering what he had to do to find the net this evening. The midfielder slipped in behind the Basque backline into space but failed to connect with a cross only yards from goal.
With ten minutes remaining the deadlock finally snapped and the hosts took a deserved lead through debutant Martin Demichelis, the defender found himself in acres of space at the near post to direct a header beyond keeper and defender on the line.
Two minutes later Malaga almost had a penalty as Duda was felled on the edge of the area wide right but his free-kick sailed straight out of play.
Malaga and Demichelis were left gutted by a cruel stoppage-time equalizer from Javi Martinez. The midfielder had come close time and time again during the match but finally managed to steer his header in off the post to save Athletic a point.
Both sides remain in the same position in the league after the draw, Malaga in 16th and Bilbao in 8th.
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