
Lazar Samardzic netted the only goal in the last minute with a superb strike from outside the box at the end of a counter attack while Marseille players were screaming for a penalty for an Ederson handball.
The result left Roberto de Zerbi’s team with three points from four games in the elimination zone in 25th place in the 36-team league, while Atalanta moved up to 16th on seven points.
Atalanta imposed their rhythm early on with crisp combinations and relentless pressing, but Charles De Ketelaere’s 14th-minute penalty – awarded after Marseille goalkeeper Geronimo Rulli brought down Nikola Krstovic in the box – was saved.
Marseille dominated the second half and thought they would be awarded a penalty when Ederson handled the ball in the box while trying to bring it under control.
On the ensuing counter attack, Samardzic curled a superb kick into the top corner, leaving De Zerbi fuming on the touchline, trying to show a replay of the handball to referee Jose Maria Sanchez.