FULHAM need a win in their final group fixture at home to Odense in a fortnight to ensure qualification for next year's knock-outs stages after a deflating night in Holland.
The Whites looked all set to collect a point, but with two minutes to go, sub Marc Janko coverted a cross and the agony was compounded when Andrew Johnson picked up a second yellow card in injury time for kicking the ball away in frustration when he was pulled up for a foul.
He will miss that game against the Danes - who at least will have nothing to play for after defeat by Wisla Krakow - but that was not the only headache for boss Martin Jol.
The gamble to rush back Damien Duff from a calf injury backfired, with the Irishman breaking down after half an hour, while Moussa Dembele also limped off.
It may not have been spectacular, but Jol's men appeared to have got the job done in Enschede - frustrating the home side for the most part, who have a fine recent home record in both domestic and European competition.
After a drab first half, the game picked up in the second half, with both sides having chances to snatch victory.
Luuk de Jong somehow headed wide from close range after being picked out by sub Ola John, the younger brother of former Fulham striker Collins John.
But at the other end, Johnson and Bobby Zamora also passed up good opportunities as the Whites sensed a late chance to secure progress to the knock-outs with a win.