The 60-year-old is a former Chile, Argentina and Sevilla coach. He has signed a contract with Marseille until June 2023.
"I have come to the end. This Thursday will be the last match," former Argentina coach Sampaoli wrote in the five-paragraph missive bringing an end to his one-year relationship with the team from Belo Horizonte.
The suspension is a likely first step towards Marseille definitively parting company with the 43-year-old from Portugal, who became coach at the Velodrome in 2019.
Ligue 1: Marseille coach Andre Villas-Boas offers to resign after being kept in dark about player transfers
The former Chelsea and Tottenham manager said the club's decision to hire Olivier Ntcham on loan from Celtic without letting him know prompted his move.
The fans, who were demonstrating against the club leadership and the team's poor recent run of results, assembled in the afternoon in front of Marseille's La Commanderie training ground, throwing smoke bombs and firecrackers.
After a strong start to the season, Marseille have dropped down to sixth place. The team is 13 points behind second-place Lille.
Ligue 1: Tino Kadewere shines as Lyon move to top with 4-1 win over Nice; Marseille held to 1-1 draw by Reims
Kadewere made an impact either side of half-time to move his side a point above Lille, who entertain third-placed Paris Saint-Germain on Sunday.
On Wednesday, after his team lost 2-1 in a Ligue 1 game in Rennes, Villas-Boas approached the journalist from Marseille-based La Provence, gave him "two unfriendly claps on the shoulder" and threatened him, according to witnesses.
Ligue 1: French clubs anticipating financial repercussions following league's termination of TV contract with Mediapro
Mediapro, a Chinese-Spanish broadcaster, has suffered deep financial problems since acquiring 80 percent of the rights for 800 million euros ($970 million) a year to broadcast from this season, in a record deal for football in France.
Andre Villas-Boas' Marseille have not won in the four matches since they beat Paris Saint-Germain last month while Lyon's winless run already stretches to five matches in the six-game-old season.
Only around 1,000 spectators were present at the Stade Velodrome due to coronavirus restrictions.
Marseille announced Tuesday the positive COVID-19 tests for three players, taking to four the number infected.
At least 37 Ligue 1 players from 11 clubs have tested positive for COVID-19 in recent weeks.
Dimitri Payet praised by Marseille president for accepting significant pay cut in fresh two-year deal
Marseille attacking midfielder Dimitri Payet signed a fresh two-year deal with the French club that runstill 2024, and has been praised by club president Jacques-Henri Eyraud for taking significant pay cuts.
According to French magazine France Football, Zubizarreta’s departure casts doubt over coach Andre Villas-Boas’ future at the club as the pair had a close working relationship
Ligue 1: Give me means to perform or I'll leave, manager Andre Villas Boas tells Olympique de Marseille bosses
Olympique de Marseille coach Andre Villas Boas has said he will not stay at the club if he is not given the means to make them competitive in the Champions League.
Marseille missed the creativity of Dimitri Payet as it dropped points in the race for a Champions League place after being held 0-0 at home by Angers
Ligue 1: Dimitri Payet's brace propels 10-man Marseille to narrow win over Lyon in violence-marred derby contest
Marseille supporters attacked the Lyon bus with stones, bottles and other projectiles on its way to the stadium, before visiting players were repeatedly bombarded with objects thrown from the crowd while taking corners during the match.
Ligue 1: Mauro Icardi, Kylian Mbappe score twice as Paris Saint-Germain outclass old rivals Marseille
Mauro Icardi and Kylian Mbappe both scored twice as Paris Saint-Germain demolished their old rivals Marseille 4-0 on Sunday in a game that further laid bare the gulf that exists between the sides and allowed the reigning champions to extend their lead at the top of Ligue 1.
Ligue 1: Marseille's sporadic run under Andre Villas-Boas continues with 1-1 draw at home against Rennes
The draw means Marseille are five points behind league leaders Paris Saint-Germain, who are two points ahead of Nantes and surprise package Angers