A 3-2 win away to Basle ensured Fulham finished second in Group E at the expense of their hosts and advance to the knockout stages. Two goals from Bobby Zamora at the end of the first half set them on their way.
Basle came out strongly after the break and reduced the arrears with a 64th minute penalty from Alexander Frei.
Zoltan Gera looked to have sealed the win with a cool finish with 13 minutes to go, although Marco Streller scored a header in the 87th minute to ensure a nervy end.