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Ngqawana, real name Zimasile, died at Charlotte Maxeke Academic Hospital in Johannesburg after suffering a major stroke.
He was 51 years old and is survived by his wife and six children.
Ngqawana was billed to perform at the Wits Great Hall on Saturday but suffered a stroke and collapsed during rehearsals at his home in Troyeville, Johannesburg.
Prominent South African jazz musicians will now perform at Wits on Saturday to commemorate "The Life and Times of Zim Ngqawana".
The jazz giant, known for his uncompromising attitude, was admitted to the hospital on Monday according to a statement released yesterday by his family.
"While rehearsing for his upcoming concert at the Wits Great Hall scheduled for Saturday, he succumbed to a major stroke.
"He was buried according to Muslim tradition last night at the West Park Cemetery in Johannesburg."
Ngqawana, who took his career seriously, created some of the most-valued and sophisticated pieces of music which was embraced by serious jazz lovers.
Mixing African folklore and complex jazz arrangements, Ngqawana was both a pioneer and originator of a deep-rooted sound that came to be known as Zimology.
Ngqawana is especially respected for his first album called Zimology. The album created raised the bar in South African jazz.
Ngqawana graduated in jazz studies from the University of KwaZulu-Natal.
He later organised a group of local musicians who received formal training in jazz studies from universities in the country.
Ngqawana performed in Europe, the US and other countries.
Promoter Peter Tladi told Sowetan that the country has lost more than just a musician.
"Zim was a friend who subsequently became a godfather to my son.
"Just two weeks ago we were together in Cape Town where he performed at the funeral of another prominent musician. He told me that he was working on a proposal for the Joy of Jazz and we were both excited by the proposal, and now this.
"This makes one wonder why our musicians are dying like this," an emotional Tladi said.
Tladi's company, T-Musicman, promotes the popular Joy of Jazz Concert that normally takes place in August. Ngqawana would have performed at the festival.
Gauteng MEC for sport, arts, culture and recreation Lebogang Maile said, "The country has lost a musical genius and the music industry is poorer.
"Zim's passing must serve as a reminder to everyone, especially the youth about the rich heritage we have.
"His music, including masterpieces such as Qhula Kwedini will continue to inspire many in the performing arts. Condolences to his family.''