Fana Tshabangu said that they were shocked to learn of Lebese's status after his death, especially his mother.
"Lebese died before he could tell his family about his status himself. We are honouring Lebese's last wish as friends of his told us Thabang always wanted to disclose his status."
The family apologised to the Gauteng department of health, and the Helen Joseph Hospital staff and management for statements that blamed the hospital for Lebese's death.
"We are satisfied with the care he received at the hospital," Tshabangu said.
Gauteng health department spokesperson Simon Zwane said the department accepted the apology and considered the matter to be closed.
Lebese's funeral was held on Friday.
The former Bafana Bafana midfielder, aged 38, died in Helen Joseph Hospital in Auckland Park, Johannesburg, last month.