The visitors started strongly, as Mason Greenwood tested Donovan Leonearly on with a vicious strike from the edge of the area that the goalkeeper had to palm away.
However, Auxerre grew into the first half and stunned Marseille by taking the lead on 34 minutes when Gaetan Perrin cut inside, beautifully curling the ball off the underside of the crossbar and into the top corner.
Theo Bair then thought he had doubled his side’s advantage just before half-time by tapping home from close range, but it was ruled out for an offside in the build-up.
Roberto De Zerbi clearly got into his players at the break as they came out quickly in the second half. Amine Gouiri was sent clean through one-on-one, yet despite beating Leon, he also sent the ball agonisingly past the post.
The forward’s luck got worse moments later when he tapped Luis Henrique’s cross home, only for the strike to be disallowed for a marginal offside in the build-up.
The task of leveling proceedings got more difficult for Marseille just after the hour mark, as Derek Cornelius was shown a second yellow after a poor challenge. Hamed Junior Traore was on the receiving end, and he then went through on goal, but Geronimo Rulli came out quickly to smother the ball well.
The goalkeeper was not as smart against Lassine Sinayoko though, as he conceded a penalty by bringing him down in the box.
Jubal Junior stepped up and sent the Argentine the wrong way, striking down the middle.
The hosts even added a third goal in stoppage time, with Junior heading in his brace from close range following a neat corner routine.
Auxerre’s win lifts them up four places into 10th in the table, and Christophe Pélissier will be especially pleased to see a clean sheet after his side conceded at least twice in each of their previous three league matches. It is only Marseille’s fifth league defeat this season but it could be a costly one as they try to chase down PSG, made worse by the fact that Auxerre did the Ligue 1 double over them for the first time since 1987/88.
Flashscore Man of the Match: Jubal Junior (Auxerre)