"Today, we have lost the best son of the nation Muzadi, a great cleric who always strived to ease tensions," he said in Kapuas Hulu, West Kalimantan.
Muzadi, who was also a member of the Presidential Advisory Board for the period of 2014-2019, died in Malang, East Java, on Thursday.
"He was the nations teacher who helped preserve Indonesias diversity. He died at 6.15 am at his residence," he stated.
The president expressed deep condolences over Muzadis death on behalf of the government and the people of Indonesia.
Muzadi, who died at the age of 73, was buried in his Al-Hikam 2 Islamic boarding school compound in Depok, West Java, in the afternoon.
He had been undergoing treatment at Lavalette hospital in Malang, East Java, for fatigue.
After three days of treatment, his condition improved and he was requested to take rest. He chose to return home to take rest.
Widodo had visited Muzadi on Wednesday and had prayed for him.
"Let us all pray for his immediate recovery. Let us hope he gets well soon," he had stated after the visit.
Muzadi was an Indonesian Islamic figure who was a nationalist as well as a pluralist.
He became the running mate of Megawati Soekarnoputri in the 2004 presidential election when he resigned as the general chairman of Nahdlatul Ulama.
As a member of the Presidential Advisory Board, he called for halting the debate over political actors taking part in the November 4, 2016, demonstration in Jakarta for the sake of the countrys unity. (*)