Atleti boss Diego Simeone was confined to the stands after being handed a four-match ban for his antics on the sidelines during their semifinal first leg against Arsenal.
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They had started well and had a great chance to open the scoring inside four minutes, Valere Germain shooting over after being slipped in by Payet.
Marseille continued to dominate for much of the first half, however, they were unable to take control of the tie as Jan Oblak was equal to much of the Ligue One sides efforts. 33-year-old goalkeeper Mandanda suffered poor communication with fullback Andre Zambo Anguissa when he cleared the ball in the 21st minute.
The final scoreline mirrored Atletico's last Europa League final win over Athletic Bilbao in 2012 and cemented their status as one of the most consistent teams on the continent since Simeone transformed their fortunes.More news: EU's Barnier: No big progress on Brexit since March
Only around 11,500 Marseille fans will officially be in attendance in a crowd of close to 60,000 and those without tickets have been urged not to travel amid fears of trouble between them and fans of Lyon.
Marseille lost its third straight European final after coming up short in the UEFA Cup final - as the tournament was formerly known - in 1999 and 2004. Payet soon succumbing to injury was another huge blow, as the France global was his team's most likely to magic a way through the super-tight Atletico defence. "We work ourselves and defend well to be a hard opponent who takes advantage of their errors".
Skipper Gabi added a rare goal late on to secure a comfortable night at the office for Atleti, who brought on Fernando Torres in stoppage time for his final appearance for the club. In the end, they could not quite deliver what would have been a real boost for French football - while Payet's injury could be a further problem for Les Bleus with the summer's World Cup now less than a month away.
"I don't know how to describe the finish (for the second goal) - perhaps cold-blooded".
"It was a dream of mine to win a title under Simeone and I told myself that this was my time".