Sampaoli, a much-travelled Argentine, replaces Andre Villas-Boas who was suspended on February 2.
McCourt, who promised “profound changes” at the club, also replaced president Jacques-Henri Eyraud, who has become a target of fan discontent, with sporting director Pablo Longoria.
McCourt said Eyraud would be joining the club’s supervisory board.
Marseille, second when last season was cut short, are seventh this season, 20 points behind leaders Lille.
“This is a new chapter for Olympique de Marseille, and I am personally committed to making it a success,” McCourt said in the statement.
“I have entrusted the presidency of the club to Pablo. His experience as sports director and talent scout is matched only by his love of the game. His main priority will be to put football back at the heart of OM.”
Sampaoli’s arrival had been expected since he requested the termination of his contract with Brazilian club Atletico Mineiro on February 22.
The 60-year-old is a former Chile, Argentina and Sevilla coach. He has signed a contract with Marseille until June 2023.
“I have been told all my life that OM is a passion. That the Velodrome lights up when the team goes to the stadium,” said Sampaoli, quoted in a club press release.
“Marseille is a people’s club and I feel myself in this heat. We’re not here to hide: we’re going to play hard.”
Marseille’s home league game against Rennes at the Velodrome on January 30 was postponed after angry supporters attacked the club’s training ground, while the players were there, in what the club called “a frenzy of unjustifiable violence”.
Eyraud, who was born in Paris, was singled out in banners hung around the city after he angered fans by talking about the “danger” of having too many Marseille residents or club supporters working at the club.
Local police said 25 arrests were made and seven officers were injured after several hundred Ultras stormed La Commanderie in a protest against the club leadership and the team’s poor run of results.
At the time McCourt called the protestors “thugs” and likened the incidents to the storming of the US Congress.
On Friday, he promised that he would visit the city “this week” to meet with fans and leaders of fan groups to “discuss his long-term plans for the club” that he bought in 2016.