Defender Sule and midfielder Sabitzer are still nursing injuries and will join the suspended wing back Daniel Svensson on the sidelines, Kovac told a press conference.
"Sabitzer and Sule, both cannot be there because of their ongoing problems. Daniel is suspended so it means we are decimated but we still have enough good players in the squad," Kovac said.
Dortmund, in 16th spot on 11 points, could still reach the top eight for automatic qualification with a win on Wednesday and a favourable combination of other results. Inter are a point ahead in 14th and have a better chance of a top-eight finish.
The top eight qualify automatically for the last 16. The next 16 teams go into two-legged playoffs in February, adding more matches to an already busy schedule for many.
"The quality in the Champions League is something special," said Kovac, whose side are second in the Bundesliga. "Tomorrow we are playing a team that has played two finals in the last three years.
"We will have to defend well but also use the chances we will get up front," said the Croatian coach. "Our stadium has an immense power and energy which we will gladly use tomorrow."
Dortmund expect a sold-out crowd of just over 81,000 on Wednesday.
"We have to play the 90 minutes with intensity, aggressiveness, dynamism and energy. We want to win and see what comes out in the end," Kovac said. "Inter have a goal as well and they can more easily reach the last eight with a win."