Klopp was given a one-match touchline ban following an angry reaction to the fourth official in their opening 2-1 defeat at Napoli in Group F. He has repeatedly apologised for his outburst.
Klopp will be replaced on the bench by his long-time assistant Zeljko Buvac.
"We have been working together for 13 years and I do not know a better coach," Klopp told reporters. "He embodies the football brain and he loves the Bundesliga and the Champions League without all the other things that come with it."
Klopp will be without suspended goalkeeper Roman Weidenfeller, who was sent off in Naples.
"It may be punishment to sit in the stands but it will not complicate matters for the team," he said. "For one game it is absolutely no problem. The only one suffering will be me."
Dortmund and Marseille both lost their opening games with the French team beaten 2-1 at home by Arsenal, who take on Napoli in north London.
"We still have lots of time to make up for lost points," said Klopp. "The winner will again have a foot in the door."
Marseille goalkeeper and captain Steve Mandanda also stressed the importance of the Dortmund game.
"We need a good result if we are to still play a role in this group," he said. "We should not be passive but try to get the best out of this game."