Family spokesperson Millicent 'Milly' Mulelu told TshisaLIVE that the family wished to distance itself from the situation.
Millicent confirmed that the family met with GBC but preferred not to go into details.
"We don't wish to comment on the incident. For us it is closed. We did speak to the church but it was a business discussion that was done in private," she said.
Millicent added that the church had apologised to the family and had distanced itself from the media storm.
"We would also like to distance ourselves from the media storm the discussions caused. We just want to honour and bury our father and uncle Joe Mafela," she said.
In the wake of the frenzy the R89,000 quote caused GBC told TshisaLIVE that it was not allowed to comment on the amount.
The church instead issued a statement explaining the way it operated. The church said that members were not charged a fee, however, the public had to pay for overheads if booked for a funeral or memorial service.
"The public has often requested the use of the facilities for memorials and funerals. As a church we only allow them the utilisation of the premises when they are available. They are required to pay for the overheads which include audio visual equipment and operators," said GBC spokesperson Dr Ezekiel Mathole.
The clergyman said that it was the church's policy to discuss quotes with organisers and families and not comment publicly on these issues.
Actor Mangaliso Ngema took to Facebook on Wednesday to make the quote public.
"We visited the Joe Mafela home last night to pay our respects. I was shocked to learn that Grace Bible Church wanted a fee of R89,000 for the memorial," he said.
The amount has since sparked a widespread debate on social media.