Klopp, who was suspended from the touchline following an outburst in their opening Group F defeat to Napoli last month, sat high in the stands on Tuesday to watch Dortmund cruise past their French opponents in style.
"It was a bit strange not having our coach around," said right back Kevin Grosskreutz. "I kept looking over to the right and he was not there and that was unusual."
"So we won this one for him because he knows exactly where to deploy each one of us."
Klopp, whose suspension has yet to be officially announced by UEFA, watched and cheered wildly as Dortmund overran Marseille in a one-sided affair that lifted last season's runners-up to second place in the group.
"The good thing is you can see a lot better from up there but it is still not something I want to do often," said the coach. "But when the game goes so well then it is bearable.
"The team applied exactly everything we had set out to do. We can always get an advantage by working more and harder and the team did exactly that."
For Bundesliga leaders and last season's Champions League runners-up the win was crucial to get their European campaign back on track as they extended their winning run at home in the competition to seven straight games.
Klopp's magic touch may have been missing in the dugout but it was clearly visible in his starting line-up with 21-year-old Erik Durm slipping in for injured Marcel Schmelzer and enjoying a flawless Champions League debut.
With Durm joining Jonas Hofmann and Marvin Ducksch as a new set of young players in the senior squad this season, Klopp is spoilt for choice despite the absence of injured captain Sebastian Kehl, Ilkay Guendogan, Lukasz Piszczek and Schmelzer.
"I am super happy with the cool way Erik set up the first goal. He could have even scored one himself on his debut. His performance was exceptionally cool."
Klopp is now faced with the dilemma of who to pick next time around.
"There are so many games coming up that the work load is that big so we will need every single player. That is why Kevin Grosskreutz will be happy when (regular right back) Lukasz Piszczek is back and Erik will be happy when Marcel Schmelzer is back."