The 58-year-old leader died between 9.30 and 10.30 pm (local time) on Wednesday, according to a report on the website of Nigerian newspaper This Day.
The late president, survived by his wife Turai Yar'Adua and nine children, would be buried on Thursday according to Muslim rites.
His aides said he was suffering from acute pericarditis and was taken to Saudi Arabia for treatment.
An information ministry official confirmed his death saying that statements would be issued later since the news came suddenly.
Born on August 16, 1951, in an aristocratic Fulani family of a former governor of Lagos state, his early education started at Rafukka Primary School and later he joined Dutsinma Boarding Primary School.
He went to Ahmadu Bello University from 1972 to 1975, earned a BSc in Education and Chemistry there, and then returned in 1978 to acquire an MSc Degree in Analytical Chemistry.
Yar'Adua became the governor of northern Katsina State after joining the ruling Peoples Democratic Party from a Leftist political background.
The late president, who took over the reins from Olusegun Obasanjo in 2007, was not seen in public following his illness since November 2009.
On his inauguration, he had promised a lot of reforms including changing the electoral system, which was considered as highly flawed.
He had also vowed to fight corruption and fight poor power supply in Africa's foremost oil producing nation where politicians are known for their corruption.
Yar'Adua articulated all these in a seven-point agenda, which he was yet to complete before disappearing from public view.
The late president succeeded in quelling the raging rebel onslaught in the Niger Delta region by granting blanket amnesty to the fighting members and promising rehabilitation.
Image: LAte Nigerian President Umaru Yar'Adua | Photgraph: Reuters