Monchengladbach have the slight advantage by virtue of a superior head-to-head record, having beaten Baup's men 2-0 in Germany two weeks ago.
However, the 57-year-old has refused to give up on reaching the knockout rounds.
"It's always painful to concede such a late goal," admitted Baup. "We scored right at the death against Fenerbahce [to draw 2-2] and now we've seen one go against us this time.
"Everything is still possible in this group if we win our two remaining games, as long as they don't win both of their games.
"We are still in with a chance of going through. To concede so late on is hard to take, frustrating, but now we need to be ready to go again when we play Nice on Sunday."
Marseille are currently second in Ligue 1.