At least one protester has died after police in Guinea-Bissau shot at crowds alleging fraud in Sunday's poll.
Kumba Yala's supporters say the polls were rigged
Some 300 supporters of former President Kumba Yala marched through the capital, Bissau, to protest at results showing he had not qualified for a run-off.
Police fired tear-gas and then live bullets at the crowds.
The election is seen as a chance to end years of instability. Mr Yala was forced from power in the most recent military coup, in 2003.
The secretary general of Mr Yala's Social Renewal Party Artur Sanha was detained.
The election commission announced on Thursday that no candidate had won 50% of the votes, so a second round run-off would be needed.
Malam Bacai Sanha of the PAIGC party, which led Guinea-Bissau to independence from Portugal in 1973, got most votes.
His second round opponent will be former military ruler Joao Bernardo "Nino" Vieira.
The United Nations Security Council has praised the election.
Malam Bacai Sanha: 158,000
Nino Vieira: 129,000
Kumba Yala: 111,000
The electoral commission did not publish the results in percentage terms but said that more than 80% of voters had cast their ballots.
The PAIGC won a majority in March 2004 parliamentary elections, which were praised as "free, fair and transparent".
Decades of instability have made Guinea-Bissau one of the world's poorest countries.
According to the UN, 80% of its population lives on less than $2 (£1.60) a day.
The next leader of this former Portuguese colony of 1.4 million people will have to find a way of reviving the sluggish economy centred on cashew-nut production.
The vote is being monitored by some 200 observers from the United State, the European Union and West African states.