Bosnia's defence will miss long-term casualty Mensur Mujdza with a broken metatarsal bone in his foot while Boris Pandza and Sasa Papac are suspended for the first leg in Zenica on Friday.
The makeshift back four likely to start against the Portuguese looked shaky in Tuesday's 2-1 warm-up win over local first division club Zeljeznicar Sarajevo, who created a hatful of chances.
"I knew very little before this game what team I would pick for the Portugal game and now I am none the wiser," Susic told Bosnian state television BHT1.
"It's not just the defence giving me a headache, it's also the midfield because we have a lot of attacking midfielders with an instinct to go forward.
"With a team structured like that, you have to score at least two or three goals to beat any opposition and that's not going to be easy against a team of Portugal's quality.
"We have two more training sessions to sort out these issues and we need to find some kind of a solution," said Susic.
"There is no doubt that Portugal are strong but we are also a high-quality team and we have to take the game to them rather than hide on the pitch and retreat.
"A goalless draw in the first leg would be a good result for us but we know we can score against anyone and I am optimistic that Portugal could be rattled by fervent home support for us in the cauldron of Bilino Polje stadium," said Pjanic.
They will be boosted by the scintillating form of captain Cristiano Ronaldo, who rifled in his fourth hat-trick of the season for Real Madrid in last weekend's 7-1 thumping of Osasuna in the Spanish league.
"There is a very wide gap between the two encounters, Bosnia have a quality team and are more mature, as is the case with Pjanic and [Manchester City striker Edin] Dzeko," said Bento.
"I predict a very balanced play-off and think each team has a 50 percent chance of qualifying.
"We will have to adapt to the stadium in Zenica and the pitch conditions so we might have to play in a different way than we usually do."
