Antoine Griezmann was the hero for Atleti as the France worldwide striker scored twice.
Marseille had been desperate to win the second European trophy in their history, on French soil, 25 years after beating AC Milan in the inaugural Champions League final in Munich.
Les Phoceens' misery never fails to crack a few smiles in Paris, despite the fact that a Europa League win would have boosted France's UEFA coefficient - helping PSG in the future.
Griezmann, who scored in every knockout round for Madrid after they dropped down from the Champions League, proved to be the difference with two smart finishes more than enough to seal the trophy. Who said modern footballing rivalries are dead? 'I hope he stays.
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Griezmann scored a second goal in the 49th minute before Gabi finished the game with Atlético's third goal in the 89th minute.
"It's about more than a trophy", Simeone said. I came back at an important moment in my life, and without doubt returning gave me a sense of balance and peace.
Jan Oblak will not push for a move away from Atletico Madrid but says the decision over his future rests elsewhere.
He athletically won a high ball in midfield and quickly swapped passes with Koke before gliding into the penalty area unchallenged and clipping the ball over the onrushing Mandanda.
Griezmann returned to France to play the final against his boyhood club and did so with a bang, scoring either side of half time to put the game beyond the reach of Marseille.