Predictions of a Jokowi presidency and strong showing by his party had helped lift shares prices and the rupiah, Asia's best performing currency this year, in the hope that it would bring a more decisive government.
The stock market, up 15 percent this year, was closed as Wednesday was declared a public holiday for the vote.
Campaigning has been notable for its lack of policy initiatives to give the economy a boost. Growth is expected to be a little more than 5 percent this year, but has weakened partly on the fall in commodity prices.
Jokowi has offered little clue to his policies but his popularity rests heavily on his no-nonsense style in running the capital, demanding his bureaucrats perform their jobs properly and by focusing many policies on improving the lives of ordinary Jakartans.
Golkar and Gerindra
The two main parties behind PDI-P, were Golkar, one-time parliamentary vehicle of the long-serving Suharto, and Gerindra which is led by ex-general Prabowo Subianto.
Early results suggest both will struggle to meet the threshold to contest the presidency, suggesting there will be intense horse-trading to form coalitions.
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Backing for the ruling Democratic Party of outgoing President Susilo Bambang Yudhoyono has fallen to single digits after it was hit by a series of high-profile graft cases last year. Yudhoyono is limited by the constitution to two terms.
Yudhoyono is Indonesia's first leader to be chosen by direct election.
"Even though we are still fixing and perfecting the system of holding these (elections), once again Indonesia can be grateful because our democratic journey is going the right way," he told reporters.
Voters, nearly a third of them under 30, chose between 6,600 candidates vying for national parliament seats. Elections were also held for 19,007 provincial and district legislative assembly seats.
Most Indonesians view parliament as among their country's most corrupt institutions, according to a 2013 Transparency International survey. Under the presidential system, however, the executive branch has the authority to overrule it.