A 67th-minute strike from on-loan midfielder Bernardo Silva made sure of the points for the principality club, marking their fourth straight league win in all competitions.
The victory ended a week that saw Monaco secure a place in the UEFA Champions League last 16 and moved Jardim's men up to sixth in the French top flight.
And, with this season's team built largely on youth rather than the expensive imports of last term, the Portuguese was quick to laud his players for coming through a stiff test against Marcelo Bielsa's men.
"It was a quality game, very intense," Jardim said. There was a lot of emotion in this derby.
"Marseille is a very physical team who, during the week, do not play in European competition. I knew this team was going to press a lot for 45 minutes.
"The second half was better. We scored and took control. It's a deserved win.
"I'm happy with four consecutive victories. I'm happy because seven players aged under 21 have played today [sic: five plus two 21-year-olds]. I have a lot of belief in them. This is the future of Monaco."
