Amid a hight turnout, election officials were preparing for a long night, handling final queues of voters, printing voting records and sealing electronic voting machines.
Al Jazeera's Marga Ortigas, reporting from a polling centre in the capital, said many voters had waited for hours outside before the centre opened at 0700 local time, to choose a new president from nine candidates.
Problems with some of the new voting machines had added to the delay, Aquino as well as some of his rivals, were also caught up in.
"It lacked prior testing so there were a lot of problems," Aquino said after casting his ballot.
A software glitch discovered a week ago nearly derailed the vote, but was fixed at the last minute.
However, some machines still malfunctioned, including in Aquino's hometown of Tarlac, north of Manila.
The authorities had expected voters to each take about 10 minutes to cast their ballots, but with around 50,000 candidates vying for nearly 18,000 congressional and local positions, many voters were taking much longer to fill in their ballots.
Omar Khalifa, Al Jazeera's correspondent in Cavite, south of Manila, said he saw a number of voters having to feed their ballot papers into the machines several times.
Despite reports of some cases of battery defects, power failures, printing flaws and memory card malfunctions, however, Khalifa said he saw about 100 votes cast into the machines and all were registered successfully.
Gregorio Larrazabal, the election commissioner, said about 300 out of 76,000 machines had problems but that most had already been replaced, adding that the problems were "not as widespread as it's made to appear".
"And what's important is that if a machine breaks down, there is a replacement and there is a back-up procedure," he said.
In past elections, manual counts delayed results for weeks and were prone to fraud.
This year, officials are hoping the new machines will speed up the process, with some early tallies expected soon after polls close.
Turnout was put at around 80 per cent of the country's 50 million registered voters.
Voters appeared undeterred by reports of scattered violence on Monday.
Troops and gunmen exchanged fire in southern Maguindanao province, where in November 57 people were massacred in the country's worst election-related attack, said army Lieutenant-General Raymundo Ferrer.
There were no casualties in Datu Salibo town but in nearby North Kabuntalan township, two civilians were killed in a clash between armed followers of rival candidates for vice-mayor, Ferrer said.
Even with the more than 30 election-related deaths in the past three months, including three on Sunday, election attacks appeared to be down.
In the 2007 vote, 130 deaths linked to elections were recorded.
In La Union province in the north, four voters were slightly wounded when a home-made bomb went off at a school being used as a polling station, police said.
Despite the blast, voting went ahead as scheduled.
In another incident in the southern city of Marawi, two bombs went off near school buildings, including one school being used as a voting centre, said Lieutenant-General Ben Dolorfino, adding that they had caused no damage or injuries.