The final election result is not likely to be known for several days.
"Voting went smoothly in most of the polling stations we visited, in spite of the late start in some places," one international poll observer said.
In the capital Cotonou, polling stations were expected to stay open until late into the night on Saturday.
Michel Allokpo, electoral commission spokesman, said voter turnout was "well over 50 per cent", lower than the 70 per cent in last year's presidential poll.
"Everything went very well. I've just voted for the candidate of my choice and I'm very happy," a woman who gave her name as Chantal said.
The election was originally set for March 25 but Benin's constitutional court delayed the vote by one week due to organisational difficulties.
Some four million Beninese were eligible to vote out of a population of 7.9 million at more than 15,300 polling stations across the west African nation.
More than two hundred domestic and international observers were present during elections.
"For me this is an occasion for celebration and I thank all the political forces in our country who are aware of the importance of this vote"
President of Benin
Voters chose 83 members of the legislature from among 2,158 candidates from 26 political parties and groups.
Yayi said after casting his ballot in Cotonou: "For me this is an occasion for celebration and I thank all the political forces in our country who are aware of the importance of this vote."
About 20 parties that back the new president have grouped together to form the Cauri Forces for an Emerging Benin (FCBE).
FCBE candidates are competing against the Democratic Renewal party (PRD), loyal to Adrien Houngbedji, the defeated candidate in last March's presidential election, and the Alliance for Dynamism and Democracy (ADD).
The ADD is loyal to Nicephore Soglo, a former president and currently mayor of Cotonou.
Corruption and poverty
Yayi inherited one of the world's poorest nations. Benin, wedged between Nigeria and Togo, has few commercial crops except cotton and that sector is currently in difficulty.
The country's economic crisis as a whole has been consistently aggravated by corruption and poor management of public funds.
The new president is popular, but his anti-corruption drive, and notably the audit he has ordered into 60 state-run companies, has made him unpopular with many politicians.
He took over from General Mathieu Kerekou, who had dominated the political scene in Benin for the past 30 years, first as a military ruler and then as a democratically elected head of state.
A few weeks ago the president's convoy came under attack north of the capital. He himself was unharmed but four members of the presidential guard were wounded.