Atletico will be looking to win their third Europa League trophy, while their French opposition will be hoping to claim their first.
Los Colchoneros booked their ticket to Lyon with a 2-1 aggregate victory over Arsenal, while Les Olympiens guaranteed their place in the final with a 3-2 aggregate win against Austrian champions Salzburg.
Here are four key battles which could determine Wednesday's clash.
4. Florian Thauvin vs Filipe Luis
Thauvin has been Marseille's best player this season with 22 goals and 11 assists in 34 league appearances. The speedy 25-year-old is likely to start on the right of a forward 3-man midfield, which means he'll come up against Atletico's experienced left back Filipe Luis.
Luis has struggled for appearances this season due to a number of injuries. The 32-year-old started only his 18th game of the season in Atletico's 1-0 win over Getafe at the weekend. Thauvin will look to exploit any signs of rustiness, but the Frenchman will also have to be wary of the threat posed by Luis at the other end of the pitch.
Los Colchoneros' full backs tend to join in with their attacks, and Thauvin isn't known for his defensive capabilities.
3. Antoine Griezmann vs Adil Rami
Antoine Griezman will be looking to score his 28th goal of the season on Wednesday. The 27-year-old already has four goals and two assists in just seven Europa League appearances.
Marseille centre back Adil Rami will be the one tasked with keeping Griezmann quiet. Rami has had a good season for the French club and, following Laurent Koscielny's serious injury, could yet be included in France's 23-man World Cup squad.
Nevertheless, the 32-year-old lacks pace - one of Griezmann's greatest assets. Rami is likely to be partnered with 30-year-old Luiz Gustavo in the centre of Marseille's defence, an area which Griezmann will, no doubt, look to exploit.
2. Dimitri Payet vs Gabi
Former West Ham midfielder Dimitri Payet missed Marseille's draw to Guingamp on Friday with a knock but is expected to start on Wednesday.
Payet has six goals and 13 assists in 31 league appearances, but the 31-year-old has been particularly instrumental to Marseille's Europa League progress having registered three goals and seven assists in 11 appearances in the competition.
He's likely to start behind striker Valere Germain and it will be up to Atletico's defensive midfielder Gabi to neutralise his threat.
1. Formations: Marseille's 4-2-3-1 vs Atletico Madrid's 4-4-2
If both managers persist with their favoured formations, then Marseille will deploy a narrow 4-2-3-1, and Atletico a traditional 4-4-2. Consequently, Les Olympiens will have the numbers-advantage in midfield, but Los Colchoneros will have more space down the sides for their full-backs to exploit.
Marseille have managed to keep just two clean sheets in their last 18 games, and their defence is particularly susceptible to set-piece deliveries and crosses from out wide - an area which Atletico excel in.
If Filipe Luis and Juanfran (or Sime Vrsaljko) can get forward without leaving themselves exposed, then Atletico and especially Diego Costa could get some joy.