Officials say the 61-year-old died of heart problems - but political opponents suspect he was sick with COVID-19.
Magufuli was one of the continent's most prominent coronavirus sceptics, encouraging people to focus on prayer instead of lockdowns and vaccines.
Vice President Samia Suluhu Hassan has taken his place on Friday, becoming the country's first female leader.
Al Jazeera's Catherine Soi reports from Nairobi, Kenya.
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