The first legs will be played on 26 April - Arsenal will be hosting Atletico as Salzburg will play guests to Marseille - and the second legs will be played on 3 May 2018. The final will be played on May 16 in Lyon.
The match-ups were decided on Friday afternoon.
The Europa League champion will get direct entry into next season's Champions League.
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Marseille, for whom captain Dimitri Payet was inspirational in their comeback 5-3 aggregate win against RB Leipzig in the quarter-finals, are now fourth in Ligue 1.
LaLiga outfit Atletico reached the semi-finals 2-1 on aggregate, despite Thursday's 1-0 loss at Sporting CP in Lisbon.
Marseille are unbeaten at home in this season's Europa League and will have the backing a fanatical crowd when they host Salzburg in the first leg.
They overturned a 1-0 first-leg deficit against RB Leipzig in the quarter-finals to prevail 5-2 in the return date and keep their dreams alive.