They have to choose between the former military general Prabowo Subianto or the Governor of Jakarta Joko Widodo, to lead the country.
Analysts are already warning that the relationship with Australia is likely to be more challenging, with both candidates more nationalist than the incumbent.
Correspondent: George Roberts
Speakers: Otis, Indonesian voter; Rika, Indonesian voter; Aleksius Jemadu, dean of political sciences, Pelita Harapan University, Jakarta; Greg Fealey, associate professor, Australian National University
(Sound of people at rally)
GEORGE ROBERTS: After months of rowdy rallies, campaigning is over, making way for the relative quiet of the polling day public holiday. But even friends are divided between the first and second candidates on the ballot.
OTIS: I think the win is the number one.
GEORGE ROBERTS: Prabowo?
FEMALE VOICES (in unison): Awwwww.
GEORGE ROBERTS: Otis's friend Rika disagrees.
RIKA: Yeah, Prabowo is the (inaudible).
GEORGE ROBERTS: The latest polling puts 14 million people in the undecided or undeclared zone. The dean of political sciences at the Pelita Harapan University in Jakarta, professor Aleksius Jemadu, says voters are weighing up two distinctly different styles.
ALEKSIUS JEMADU: Look at how Joko Widodo make his campaign. He present himself as a humble leader, more people-oriented.
GEORGE ROBERTS: But there's also a sense that Indonesians want a firmer hand after a decade of president Susilo Bambang Yudhoyono.
ALEKSIUS JEMADU: Prabowo campaign, the emphasis is more on high profile, the leader of a strong nation. He emphasise more on the nationalistic overtones of his campaign, of his foreign policy as well.
GEORGE ROBERTS: Associate professor Greg Fealy from the Australian National University says, either way, Australia's relationship with Indonesia is set to become trickier.
GREG FEALY: I think it's going to require the Australian Government to rethink its approach to Indonesia. And it's going to have to factor in the likelihood that a future Indonesian government will be far less inclined to forgive Australia any of its sort of domestically driven, political policy initiatives towards Indonesia.
GEORGE ROBERTS: Both candidates are more nationalist than president Yudhoyono.
GREG FEALY: Neither of the two candidates in the current presidential election in Indonesia are as statesman-like and both of them have a far more overtly nationalist agenda.
GEORGE ROBERTS: While the most recent opinion polls show a slim margin between the two men, Jakarta's stock market rose for the second day in a row on hopes that Joko Widodo would win.
Greg Fealy thinks he would be an easier president to deal with.
GREG FEALY: He's a more stable person in his personality and he is more pragmatic and I think more measured. Prabowo Subianto is a much more difficult person to predict because his range of behaviour is far wider and he is extremely temperamental.