Being down 2-0 in the first match, Salzburg came out firing as Amadou Haidara's great solo effort gave the Austrian team the lead in the 53rd minute.
Both Olympique de Marseille and Nice are in need of the points when the clubs meet at Orange Vélodrome on Sunday evening hoping to pursue their European ambitions.
The pressure nearly paid off when Florian Thauvin might have been awarded a penalty when his shot clearly hit Duje Caleta-Car's arm.
The French outfit went in search of a goal for the remainder of the second half but were unable to bypass the Salzburg defence as the game went into extra time.
Should Marseille have been given a corner? .
Salzburg celebrate their second goal after they level things up on aggregate on Thursday
The set-piece that led to the winning goal was contentious as Salzburg thought the ball had come off a Marseille player last.
Yohann Pele (Marseille): Pele won back his place in football after two years out with a pulmonary embolism. Aaron Ramsey bundled his way through but the ball would not fall for him six yards out while Mesut Ozil flashed too sumptuous deliveries across the face of goal. Subs: Pongracic 6, Minamino 6, Hwang 7.
Several Marseille players, including Steve Mandanda, Florian Thauvin, Dimitri Payet, Adil Rami and Bouna Sarr, have a chance to be included in Deschamps' squad, while Atletico forward Antoine Griezmann is all but guaranteed to travel to Russian Federation.
Lucas Ocampos was taken off with a knock shortly after the restart to be replaced by Zambo Anguissa, but Garcia rebalanced his team on the hour mark as Njie was brought on for Lopez.
The predatory talents of Antoine Griezmann and Diego Costa aren't liable to be as forgiving deep behind enemy lines as Salzburg were, and Marseille will struggle if they focus too heavily on preserving a clean sheet in Lyon. The Norweign striker has scored 16 goals this season. Haidara's cross found its way to Xaver Schlager whose shot was going off target until it hit the toe of Marseille defender Sarr and went in.
99' - PELE STOP - Caleta-Car stoops to reach a cross from the right, and thunders a header at goal.
Haidara was dismissed for a second yellow card after lashing out at Payet, with Rose storming onto the field at full-time to confront referee Sergei Karasev and his officiating team. A second yellow for lashing out at Payet with his arm.
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