The Portuguese forward, who returned earlier this month following two months out with an ankle problem, tormented the Marseille defence throughout, netting a clinical double.
"Cristiano Ronaldo was the best player on the pitch," the Marseille-born Zinedine Zidane, now an adviser to Real president Florentino Perez, told reporters.
Ronaldo, sent off for Real at the weekend, put the Spanish side in front after only five minutes, firing a fine 30-metre free kick into Steve Mandanda's top corner.
He wrapped up the win with 10 minutes left after pinching the ball from the Marseille keeper before coolly slotting home.
"We know he is a great player and a great professional," Real coach Manuel Pellegrini told reporters.
"I had already said he would not be affected by his sending off last weekend in La Liga. He has this capacity to spring from everywhere and score."
Ronaldo had an odd weekend as he missed a penalty, scored a goal, set up another and picked a red card for a second bookable offence in a 4-2 defeat of Almeria on Saturday.
The former Manchester United player was unstoppable at the Stade Velodrome, twisting Marseille defenders inside-out on both flanks with his acceleration and some exquisite turns.
"I feel better and better and not only because I score goals. I feel better in the game. Everything is fine," said Ronaldo, who is suspended for this weekend's clash with Valencia in La Liga.
"This match will do him good mentally," said Pellegrini. "Too bad he will not be there for the Valence game."
