The Maulana was expected to leave for Medina, another holy city 340 km north of Mecca, on November 18, but fell ill and was admitted to a hospital.
He suffered from fever and kidney failure and passed away at 10 am on Sunday, B R Abdul Wajid, an associate of the Maulana, said.
His wife Dilnigar Shaheen, daughter Sumbula, and son-in-law Majid Khan had accompanied him for the pilgrimage.
The Maulana was buried at the Jannatul Mu’alla burial ground in Mecca late Sunday night. He is survived by wife, three daughters, and a son.
The Maulana had been serving at the City Jamia Masjid since 1983.
Several Muslim organisations have expressed their condolences.
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