The situation illustrates the difficulty when companies are closely tied to a single person, and that Papa John's may need to publicly distance itself further from Schnatter after dealing with backlashes brought about by his comments.
Laundry Service cut ties with Papa John's shortly after.
Several players had expressed a desire to have the Papa John's name removed from the stadium. The right to change the name of the stadium reportedly belonged to Schnatter.
The decision came Thursday morning by AMB Sports & Entertainment which owns the teams and oversees the operations at Mercedes-Benz Stadium.
John Schnatter quits as chairman after using racial slur during a conference call on how to handle controversial situations.
A team spokesperson said in a statement that there will be no more partnership with the Kentucky-based company, but that the team remains "supportive of our local operators who have been fantastic partners for more than eleven years".
The pizza chain later said it had accepted Mr Schnatter's resignation and that a new chairman would be appointed in the coming weeks. The company had a strong relationship with the University of Louisville, but on Wednesday, the university announced Schnatter had resigned from its board of trustees and it would consider re-naming its Papa John's Cardinal Stadium.
It has also been decided he will no longer be in any of the advertising or marketing materials associated with the brand.
The CEO of Papa John's released a statement regarding comments made by the founder and former CEO John Schnatter.
That prompted the company's stock to recover some of the losses it suffered after the report, and shares were up 1% Friday.
A person inside the company with knowledge of the decision said the decision to remove Schnatter as the marketing face of Papa John's was made by top executives and the details and exact timing are still being worked out.
Schnatter resigned from his company on July 12 after taking flack for using the n-word during a training session on workplace behavior.
Bendapui said at a news conference Friday that "there's too much hurt around" the Papa John's name right now.