The German side nicked a point from a see-saw encounter at the Stade Velodrome.
Moments after Marseille's Loic Remy had headed against the crossbar, it was Gladbach who struck first through Mike Hanke.
Joey Barton's goal direct from a corner levelled it seven minutes into the second half and Jordan Ayew turned the game on its head by giving Marseille a 67th-minute lead as their pressure told.
But Marseille were denied the three points when Arango fired home in the 93rd minute for a somewhat fortunate Gladbach side.
Remy was inches away from opening the scoring in the 14th minute when he got up to head Benoit Cheyrou's corner against the crossbar.
Five minutes later, Gladbach led as Arango teed up Hanke to finish from close to the penalty spot.
Marseille poured forward in search of an equaliser, but Andre Ayew missed the target and Morgan Amalfitano's volley was charged down by Roel Brouwers. Andrew Ayew then headed wide from a Barton cross.
They had to wait until the 52nd minute for the leveller to come, and it came in stunning circumstances as Barton's corner from the left wing curled all the way in at the far post as Gladbach goalkeeper Marc ter Stegen failed to distinguish himself.
Marseille smelled blood and the pressure continued, with Jordan Ayew firing narrowly wide from the edge of the area.
They got their second in the 67th minute when Jordan Ayew found the top corner from the edge of the area.
Rod Fanni then blazed over as they tried to put the game to bed, but their failure to do so cost them at the death as Arango got on the end of Lukas Rupp's late cross to blast home.
The result leaves both sides on five points in what looks to be a straight battle for second place, with Fenerbahce clear on 10 points and AEL Limassol on one.