Barton suggested on Wednesday that Silva is a transsexual before PSG threatened to take legal action against the 30-year-old Englishman.
"L'Olympique de Marseille and Joey Barton wish to apologise to Thiago Silva and his club for the inappropriate statements held by the English player on social networks during the past 36 hours," read a club statement.
"This morning, the management asked Olympian Joey Barton to put an end to the controversy which opposed him to the Brazilian defender.
"The Olympian midfielder pledged to immediately cease the posting of any derogatory statements against Thiago Silva."
Barton is currently on loan at Marseille from Queens Park Rangers until the end of the season.