The start of Marseille's season was thrown into chaos on Saturday when Marcelo Bielsa resigned following defeat to Caen on the opening weekend of the French top flight.
Bielsa's future at the club had been uncertain but, following his departure, Klopp was touted as a potential replacement.
The German enjoyed seven successful years at Signal Iduna Park before departing at the end of last season, with a poll from French newspaper L'Equipe this week showing him as many people's ideal choice to replace Bielsa.
However, Klopp's agent Marc Kosicke told Bild: "Marseille has expressed great interest, but for Jurgen the time has not yet come for him to come back."
Klopp won two Bundesliga titles and the DFB-Pokal while at Dortmund, while also leading the club to the final of the UEFA Champions League in 2013.