Almunia, Wenger's regular No.1, has been ruled out of the first leg, away at the Estadio do Dragao, with a finger injury, meaning Fabianski will make a rare start.
The 24-year-old was sidelined with a knee injury at the beginning of the season and has made just five starts during the campaign. But Wenger has full confidence in the Polish goalkeeper.
"I believe that Fabianski is top, top level and has massive potential," said Wenger. "It is not easy for a keeper to come in and out.
"What he misses at the moment is the number of games, but I have no doubt about his potential."
Sol Campbell looks set to make a first Champions League appearance since the 2006 final defeat to Barcelona.