Zamora is a doubt for the biggest match in the club’s 131-year history with the Achilles injury that required a pain-killing injection two weeks ago.
Fulham’s top scorer with 19 goals trained on Monday but failed to join his team-mates for the eve-of-match run-out at the Hamburg Arena.
Other than Zamora the whole squad participated, including in-form winger Damien Duff, who has been battling with a leg injury.
Earlier, manager Roy Hodgson expressed his hope that Zamora and Duff would be available to face Atletico but now faces an anxious wait on the former.
“Both players trained yesterday and that was very positive,” said the Fulham boss.
“I’ve been given no indication that they’re suffering from a reaction so my hope is that they’ll be available tomorrow.”
Hodgson has his heart set on emulating Bobby Robson by becoming the first English manager to lift a European trophy for 13 years.
Fulham hope to defy the odds one last time when they meet favourites Atletico.
The last time an Englishman tasted success while guiding a club in European competition was in 1997 when Robson led Barcelona to glory in the Cup Winners Cup.
“To follow a manager like Bobby Robson would be fantastic because as you know, we were friends for many years,” he said.
“He was a great man, a great manager and it would be very nice to think I could follow him.”
It has been 25 years since an English manager won a European competition while in charge of an English club with Howard Kendall winning the Cup Winners Cup at Everton.
Hodgson, whose outstanding season has seen him linked with a move to Liverpool, offers a simple explanation for the lack of success.
“The best English teams don’t have English managers and the best foreign teams don’t have English managers,” he said.
“Therefore, you’re looking for an English manager to win a trophy with an unfancied team.
“If you’re really serious about winning a title at this level, especially the Champions League, then you must make sure you’re working for big clubs because it’s not very often that teams like ours get to the final.”
A Fulham triumph would taste all the sweeter knowing they have done it the hard way.
Qualifying started 10 months ago and their astonishing march to the final has spanned 18 matches, including contests against Shakhtar Donetsk – the winners in the competition’s previous guise as the UEFA Cup – German champions Wolfsburg and Italian giants Juventus.
Victory would also cap a special campaign for Hodgson, who has been showered with praise for his achievements at Fulham in his second spell in the Barclays Premier League.
“If we lose then I hope it means we’ve been beaten by a better team and not that we’ve been very unlucky or been hit by some decisions that are controversial,” said Hodgson.
“At the moment we’re planning not to be second best, we’re planning to try and win the competition.
“Whatever happens it’s been a very good season for us.”
FULHAM: Schwarzer; Pantsil, Hughes, Hangeland, Konchesky; Duff, Murphy, Etuhu, Davies; Dempsey/Zamora, Gera.