Spanish coach Oscar Garcia announced late on Tuesday that he has resigned as first team oach from the Greek super League side.
"I decided, with the agreement of the club, to finish our cooperation today to give the team more time to prepare for the next season," said Garcia, who spent only three months in the job.
Marinakis, who also owns English second-tier side Nottingham Forest, acted on Monday after Olympiakos fell nine points off Greek Super League leaders AEK Athens following a 1-1 draw on Sunday with Levadiakos.
With just four games to play, that virtually ended Olympiakos's hopes of winning a record eighth straight title.
Marinakis vowed to call up players from the club's under-20 team to play the remainder of the season, while he fined the first-team squad 400,000 euros ($490,000).
Garcia's brief reign was a turbulent one.
Having left French side Saint-Etienne in November, he became the club's third coach of the season when signing an 18-month deal in January, but failed to spark their bid to retain the title.
Things got worse in February when he was hit on the head by a cashier's roll thrown by a PAOK supporter before a league match.
The 45-year-old was taken to hospital as the game was abandoned, with Olympiakos later awarded the victory.
But, like title rivals PAOK, the club also fell foul of football authorities when they were docked three points over crowd violence during their 2-1 defeat to AEK.
And last week, a group of Olympiakos supporters fought with riot police during a protest against perceived Greek government favouritism for their rivals.
In a brief announcement, Olympiakos thanked Garcia for "his contribution to the club" and wished him "every success in the future".
A former Barcelona player, Garcia made his name in coaching by winning the Israeli league with Maccabi Tel Aviv in 2013 and then leading Red Bull Salzburg to successive Austrian league and cup doubles in 2016 and 2017.
He also coached English clubs Brighton and Watford.
Meanwhile, Olympiakos's traditional rivals Panathinaikos, who have fallen on even harder times, were docked three points by the Greek league for failing to pay off debts to their former German defender Jens Wemmer.
It's the second time this season they've been hit with a penalty having also lost two points over fan behaviour in a match last season against PAOK.
Panathinaikos owe Wemmer 498,322 euros in unpaid wages.
The 20-time champions will now drop to 11th in the 16-team league. They have been in financial difficulty since wealthy media and ship owner Giannis Alafouzos abandoned the club at the start of the season.