The 28-year-old, who was linked with a move to Newcastle United in the summer, will now remain with the Ligue 1 outfit until at least 2017.
A statement on the club's official website read: "After arriving at the club from Libourne-Saint-Seurin in 2006, the French international is now under contract with l'OM until 2017."
The French international told reporters: "I am delighted to sign a contract with Marseille. Fenerbahce wanted me but they could not agree with Marseille. I will play for this great club any time they need me."
Valbuena has scored four goals for his country.