The French side went into Thursday's semi-final with a 2-0 lead from the first leg, but their hosts scored twice to take the game into extra time.
But Marseille struck deep into the added period from a corner Salzburg felt was incorrectly awarded, Andre-Frank Zambo Anguissa's shot appearing to deflect wide off a Marseille team-mate. Marseille were otherwise very poor, allowing Salzburg to cut the two-goal deficit.
And Marseille didn't have to wait long.
Eight minutes into the second half, Salzburg pulled a goal back thanks to a strike from young midfielder Amadou Haidara to make it 1-2 on aggregate.
Berisha has a solid share of his team's set pieces, giving him a strong floor, especially in this week where Salzburg must come out and attack.
The Marseille-born striker, who is due to start in place of injured Kostas Mitroglou, told AFP he'd often experienced these fallow spells but that hasn't diminished his confidence "because I've also had fantastic months, like last August, or between December and February when I was scoring all the time". Minutes later, only an unbelievable stop by the 35-year-old Pele prevented Hwang Hee-chan from putting Salzburg ahead. "I wanted to play against Marseille in the last 16, quarter-finals or semi-finals to play at the Velodrome, but sometimes things don't go the way we want them to", he told "L'Equipe".
Marseille goalkeeper, Yohan Pele, made an outstanding save to keep out Duje Caleta-Car's header from a corner in the extra time.
With both sides suffering from exhausted legs, the tie seemed to be headed to penalties when Marseille won a corner in the 116th minute. Fans of the French side celebrated securing their first European final appearance since 1999 by taking to the streets around the port city.