Jose Mario Vaz of the African Party for the Independence of Guinea-Bissau and Cape Verde (PAIGC) came first in Sunday's ballot with 40.9 per cent of the vote while Nuno Gomes Nabiam garnered 25.1 per cent.
Almost three-quarters of Guinea-Bissau's eligible voters turned out for the watershed elections, called to turn the page on years of political instability and military violence.
The election, which marked the first presidential and parliamentary polls in the west African nation since a military coup in 2012, will go to a run-off between the two leading candidates scheduled for May 18.
The United States praised the holding of successful elections as an "important step" towards a better future for the country of 1.6 million people.
Meanwhile United Nations Secretary General Ban Ki-moon applauded Bissau-Guineans for holding peaceful polls with high voter turnout, saying they had "clearly expressed their desire for the full return to constitutional order in their country".