Barton made the comment on his Twitter feed Tuesday and commented about Silva again the following day. The Marseille midfielder faces a hearing on April 15.
Marseille released a statement on Thursday apologizing for "the inappropriate comments" and said it "asked Joey Barton to put an end to the attack on PSG's Brazilian defender."
The club added "the Marseille midfielder pledged to immediately cease the posting of anything derogatory about Thiago Silva."
PSG called the comments "unacceptable" and it could take further action.
Barton was riled by comments this week by Silva alluding to the former England international.