Rafael Correa, a former finance minister who has rattled investors with talk of debt default, had led the electoral race, but Alvaro Noboa gained momentum in the final weeks of campaigning with his populist, free-market platform.
Noboa won about 27 per cent of votes while Correa won about 22 per cent, according to partial official results.
If no candidate wins more than 50 per cent of votes or 40 per cent of votes with a 10 percentage point advantage, a run-off between the two contenders will be held on November 26.
After three presidents were ousted in the last ten years, many Ecuadoreans see their political class as inept and corrupt. More than half of the population of 13 million live in poverty, many of them in rural indigenous communities.
An economic crisis in 1999 forced the world's number one banana exporter to default on its foreign debt and assume the dollar as its currency. Last year, unrest forced Lucio Gutierrez, the then-president, from office charged with abusing his authority.
Although little known until earlier this year, Correa, has soared in the polls as Ecuadoreans, fed up with the traditional political class, were impressed by his anti-establishment message and promises to sweep away the political old guard.
His association with Hugo Chavez, the Venezuelan president, and his promises to disband the discredited Congress and restructure Ecuador's sovereign bonds have sent ripples through Wall Street and Washington, which is locked in an ideological standoff with the Venezuelan leader.
Voters are also electing a new 100-member Congress and hundreds of local government posts.
Correa has promised a vote to rewrite the constitution and curb old parties with a "citizen's revolution".
He opposes a US free trade deal and wants to stop the US military operating in Ecuador.
Noboa lured voters with promises of jobs and housing for the poor during a populist campaign in which he handed out wheelchairs, medicine and even cash. He played successfully on fears that Correa could roll back economic liberties.
A second round between the two candidates could be close. Noboa may draw on support from traditional parties such as the Social Christians who see Correa as a threat to their influence. But Correa has appealed across the classes.
Michael Shifter at the Inter-American Dialogue think tank said: "Both are anti-political candidates taking advantage of the discredited political establishment in Ecuador even if they are on different ends of the political spectrum.
"Whoever wins in the second round this is not exactly a recipe for stability."