Earlier, his second namaaz-e-janaza was held at the National Eidgah in the morning.
The first namaaz-e-janaza of the former president was held at his village home in Pemoi of Paikura union in Kendua upazila, Netrokona.
The former president breathed his last at the Combined Military Hospital in the capital at around 10:28am on Saturday.
The 92-year old Shahabuddin Ahmed was suffering from old age complications.
Born at Kendua of Netrakona on 1 February 1930, Shahabuddin Ahmed was appointed Chief Justice of Bangladesh on 14 January 1990.
He later became the head of the government as acting president of the country after the fall of HM Ershad in 1990. Shahabuddin Ahmed formed a caretaker government with neutral non-political persons that oversaw the general elections in the country in February 1991.
Justice Shahabuddin was elected the president of the country unopposed on 23 July 1996 having been nominated by the Awami League.