Fans were asked to leave the stadium calmly.
"Following the injuries of Lyon members, considering the opinion of the club, which did not wish to start the match, and the established protocol, the decision was taken not to play the match," said referee Francois Letexier, quoted by French media.
"The images of the OL bus attacked with stones and its supporters, and of Fabio Grosso's blooded face, are appalling," French sports minister Amelie Oudea Castera said on social media platform X, formerly known as Twitter.
"These unacceptable acts deny the very values of soccer and sport, and the perpetrators must all be found and severely punished," she added.
Seven suspects had been arrested on Sunday night, the minister added.
Marseille said it accepted the decision taken by the French Professional League to call off the game, pledging to make sure it could "take place at the Stade Velodrome as soon as possible and under the best possible conditions".
"Because of a handful of thoughtless people, the party planned for this evening has been ruined, and 65,000 fans have been deprived of attending a football match," the club added.
Lyon said Grosso and his assistant, Raffaele Longo, were hit by projectiles, resulting in serious injuries to their faces, adding that six buses carrying supporters were also targeted.
"Olympique Lyonnais regrets that this type of situation occurs every year in Marseille and calls on the authorities to take the seriousness and the repetition of such incidents into account before an even more serious tragedy occurs," Lyon said.
Lyon are currently bottom of Ligue 1 with three points after nine matches. Marseille are ninth with 12 points.