Siasia was chosen ahead of his former captain Stephen Keshi, the Nigerian Football Federation (NFF) confirmed.
"After careful deliberation, the NFF has accepted the recommendation of the technical committee that Samson Siasia be appointed as head coach of the Super Eagles," the NFF said in a statement.
"Importantly, this is subject to a contract to be executed in a couple of days."
Siasia will succeed Swedish coach Lars Lagerback who rejected an offer to remain at Nigeria's helm following their first-round exit from this year's World Cup finals in South Africa.
Austin Eguavoen has been in charge of Nigeria on a temporary basis during the past few months.
Siasia will take up the post from December 1 but will travel with Nigeria for a friendly against Iran on November 17.
The 43-year-old has been working with Nigerian side Heartland, who played against Egyptian duo Ahli and Ismaili in this season's African Champions League.
His first task will be to qualify Nigeria, who last won the competition in 1994, for the 2012 African Cup of Nations.
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