His rival, Bruno Amoussou, finally agreed to take part in the second round of the elections after the departure of former President Nicephore Soglo and parliament speaker Adrien Houngbedji from the contest.
Reports from the main city, Cotonou, said only a trickle of voters had gone to the polling stations by late morning - in contrast to the queues seen in the first round.
President Mathieu Kerekou faces one of his own ministers in after two well-supported candidates from the first round declined to stand again, saying they did not want to legitimise elections they believed to be heavily flawed.
Mr Kerekou is widely expected to beat rival candidate, Bruno Amoussou, with the elections having been marked by accusations of corruption and incompetence.
President Kerekou seized power in a coup in 1972. Voted out in 1991, he won a surprise election victory in 1996.
Apart from a five-year absence in the early 1990s, he has dominated political life in Benin for most of the past 30 years.
His rival, Bruno Amoussou, finally agreed to take part in the second round of the elections after the departure of former President Nicephore Soglo and parliament speaker Adrien Houngbedji from the contest.
The whole election process as been marked by rows and recriminations.
Nine members of the national electoral commission, Benin's constitutional court, have resigned after the body was fiercely criticised for giving out false results.
A huge number of votes appear to have gone missing.
Great survivor
Benin's press has given a highly negative account of what now appears to be something of a national embarrassment.
But Mr Kerekou will probably ride out any criticism.
He first came to power as an angry young army officer in a coup staged in 1972.
He is now one of Africa's great survivors.