Borussia Dortmund qualified as Group A winners for the Champions League last 16 after beating Thierry Henry's Monaco 2-0 on Tuesday.
Portugal's Raphael Guerreiro scored twice to claim all three points for the visitors as Atletico Madrid could only draw 0-0 at Club Brugge.
Lucien Favre made nine changes from Saturday's derby victory against Schalke which continued their superb unbeaten start to the Bundesliga season.
"It's a perfect evening. On the whole it was a deserved victory," Favre said.
Henry started four teenagers in a meaningless game for the Ligue 1 strugglers who were guaranteed to finish bottom of the group for a second straight campaign after defeat at Atletico in round five.
The former France striker stated he used the fixture as a warm-up for Sunday's domestic trip to Lyon.
"Dortmund posed a real challenge. We'll recover quickly and prepare for Lyon," he said.
"Right now we have a problem, to sort things out in Ligue 1."
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