The Jakarta market ended down 3.16% after the Indonesian Democratic Party of Struggle (PDI-P) came first with around 20% of the vote in Wednesday's polls, according to unofficial tallies.
But while the PDI-P won -- and its popular presidential candidate, Jakarta governor Joko Widodo, is on course to be the country's next leader -- the results suggest it will have to form a large coalition government.
A party or coalition of parties needs at least 25% of the national vote, or 20% of 560 seats in the lower house of parliament, to field a presidential candidate in the July election.
The result increased "the chance that any coalition which comes into power may consist of an unwieldy group of parties, rather than just two or three with reasonably similar political platforms", said Wellian Wiranto, an economist from OCBC bank, in a note.
Analysts have warned such an outcome could stall much-needed economic reforms in the country.
Mr Wiranto said that parliament could split into small factions, as has been the case under the current six-party coalition headed by President Susilo Bambang Yudhoyono's Democratic Party.
"Many decisions will be hard to make," Umar Bakry, executive director of pollster Lembaga Survei Nasional, told Dow Jones Newswires.
Economic growth in Indonesia dropped to a four-year low in 2013, and while external factors played a role, the government has also been criticised for failing to push through reforms, often due to conflicts between coalition partners.
Meanwhile, other Asian markets rose, taking their lead from a Wall Street rally after minutes from the US Federal Reserve's latest policy meeting showed no support for an early rise in interest rates.
While early gains were pared after China said imports and exports fell sharply in March, Hong Kong was lifted by hopes of new government stimulus and news of a plan to increase access between the two cities' stock exchanges.
Tokyo ended flat, edging up 0.43% to 14,300.12, and Hong Kong rose 1.51%, or 343.79 points, to 23,186.96, while Manila rose 0.78%, or 51.40 points, to 6,638.89.
Regional investors were given a positive lead from the United States after the Fed minutes showed bank policymakers were broadly in favour of continuing a steady reduction in its stimulus programme.
The news eased fears of an early rise in rates. Last month stocks sank after Fed chief Janet Yellen suggested rates could go up in early 2015, earlier than most analysts had expected.
"There's been this overriding fear in the market that tightening would be sooner on the horizon than people imagine," said Brent Schutte, market strategist at BMO Global Asset Management.
"Today's minutes walk back some of those fears."
The three main indexes on Wall Street climbed for a second successive day on the back of the minutes.
The Dow rose 1.11%, the S&P 500 advanced 1.09% and the tech-rich Nasdaq rose 1.72%.
China said Thursday that imports slumped 11.3% year-on-year and exports fell 6.6%. Expectations had been for imports to rise 2.8% and exports to increase 4.2%.
The news adds to increasing uncertainty about the Asian economic giant and key driver of global and regional growth following a string of weak indicators, including those on investment and industrial output.
It also led a Customs spokesman to admit: "Currently our foreign trade indeed is having some difficulties."
He added that trade had been hit by rising competition from neighbouring countries as well as "friction with major trade partners".
However, Chinese investors took the figures as an opportunity for Beijing to unveil further measures to kickstart economic growth following last week's mini-stimulus.