The president had been suffering kidney and heart ailments for the past several month, during which acting president Goodluck Jonathan had taken charge.
With the president succumbing to his illness, the acting leader will be sworn in as the president of Africa's most populous nation.
The country turned a democracy about a decade ago. The constitution, therefore, requires Jonathan to be sworn in as head of state and to appoint a new deputy.
The presidency will be announced after seven days of national mourning.
Umaru Yar'Adua will be buried in his northern home state of Katsina at 2 pm on Thursday, May 6.