Duff hobbled off at half-time during the Barclays Premier League defeat with a leg muscle injury. The winger has been an integral part of the Cottagers' European campaign, which has seen them brush aside the likes of Juventus, Shakhtar Donetsk and Wolfsburg to reach Wednesday's final in Hamburg.
"Duff was taken off at half time because he took a kick a while ago and we think one of his muscles was cramping up," said Roy Hodgson. "That was a blow of course. We hope it's not too serious. I hope he'll be fit for the final."
The Republic of Ireland midfielder did emerge after the final whistle to take part in a lap of appreciation for the Fulham fans following the club's last home game of the season.
He will now be monitored by the club's medical staff, who are already working overtime to make sure that top goalscorer Bobby Zamora is fit for Wednesday's final.
Hodgson added: "There's a week to go now. The medical staff don't think it's a muscle tear or anything like that. They think that it's something to do with a kick he took a while ago which is switching off the muscle."
Zamora's physical presence was sorely missed by Fulham's attack on Wednesday night as Hodgson's team slid to their fifth home defeat of the season with a sub-par performance.
The former Spurs striker has scored 19 times this season, including eight in Fulham's European campaign.
Hodgson revealed that the 29-year-old is struggling to overcome the Achilles injury which has kept him out of the Cottagers' last two matches.
Hodgson said: "Bobby stands a chance of making it but he's not making vast amounts of progress on a daily basis so it could be touch and go."