The party secured about 19% of the vote, unofficial tallies show.
But it is not clear if it will meet the 25% voting threshold to enter Jakarta Governor Joko Widodo in the 9 July presidential election by itself.
The official election results will be announced in May.
Some 19,000 seats were contested across Indonesia in Wednesday's polls, including the 560 seats in the national parliament.
A poll by Jakarta think tank, the Centre for Strategic and International Studies (CSIS), put the opposition Golkar party in second place with 14% of the vote, followed by the Great Indonesia Movement Party with 12%.
Islamic parties also appeared to have performed better than expected, together grabbing about a third of the national vote.
Support for the ruling Democratic Party of Indonesian President Susilo Bambang Yudhoyono - who cannot serve a third term as president - fell by half. His party came in fourth with 10% of the vote.
Unofficial tallies were based on samples from around 2,000 polling stationsMr Yudhoyono told reporters that he respected the early results.
"Let's honour the result of this election and be ready to accept new national leadership that will lead the nation to be better," the Associated Press news agency quoted him as saying.
CSIS political analyst Philips Vermonte told Reuters news agency: "Parliament is likely to be very fragmented because many parties have gotten a relatively big share of votes."
Political uncertaintyThe parliamentary polls are key to deciding which parties can field presidential candidates. Parties must either secure 25% of the total vote or 20% of the seats in parliament.
Candidates whose parties fail to meet these thresholds must form or enter a coalition before they can run for president.
Indonesian stocks fell over 3% on Thursday, after expectations PDI-P would secure enough votes to put Mr Widodo, the Jakarta governor, straight through to presidential polls were dashed.
"We see the possible formation of a weak government with limited ability to push through necessary reforms and policies ahead," Bahana Securities research head Harry Su told Reuters news agency.
Mr Widodo is seen by many as Indonesia's next president. He told reporters on Wednesday that his party was "widely open" to a coalition.
"It is not possible for PDI-P to work alone. We have to co-operate with those having the same platform," he said.