The guitarist, producer and vocalist rose to fame when he featured on Paul Simon's Graceland album in 1986.
He was admitted to hospital a few days ago, while a public appeal was launched to help pay for his medical bills.
In an interview with The Sowetan newspaper earlier this month, Phiri said: "Let me suffer [in peace with my] pain, on my own with my dignity."
Tributes have been pouring in for Phiri on Twitter, with people using the hashtag .