Both won more votes than Mr Amoussou, but said they did not want to legitimise an election they believed was flawed.
The country's autonomous electoral commission said he took 84% of the vote.
The result was announced on Saturday after cabinet minister Bruno Amoussou - the only challenger remaining in the race - conceded defeat.
Former President Nicephore Soglo, and the Speaker of Parliament, Adrien Houngbedji, both withdrew after the first round of voting, which they described as a "masquerade".
Both won more votes than Mr Amoussou, but said they did not want to legitimise an election they believed was flawed.
Turnout for the second round of voting was low, with reports saying that, in the capital Cotonou, only a trickle of people went to the polling stations.
This is in contrast to the queues seen in the first round.
Mr Amoussou nevertheless congratulated Mr Kerekou on a "clean victory".
Great survivor
President Kerekou seized power in a coup in 1972. Voted out in 1991, he won a surprise election victory in 1996.
Apart from that five-year gap, he has dominated political life in Benin for most of the past 30 years.
The whole election process this time round has 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.
Benin's press has given a highly negative account of what now appears to be something of a national embarrassment.
But observers say Mr Kerekou will probably ride out any criticism.