Golkar displaced President Megawati Sukarnoputri's ruling Indonesian Democratic Party of Struggle (PDI-P) with a thin but progressively widening lead of 79,395 votes.
Golkar's total now stands at 15,231,572 votes or 20.43% of the 74.5 million votes tallied, according to election commission figures.
It was still not clear when the computerised count would end. More than 147 million people were eligible to vote in the legislative polls on 5 April in the world's third largest democracy.
No official turnout figure has been given, but some estimates put it around 80%.
Golkar itself and four election study groups have already predicted it would emerge the largest party, less than six years after Suharto stepped down. But so far it has failed to match its performance in the last polls in 1999 when it won 22% of the vote.
PDI-P meanwhile has suffered a dramatic slump in support compared to the 34% it won in 1999. Analysts say Megawati faces a tough battle for re-election in July as a result.
Third was the National Awakening Party (PKB) of former president Abdurrahman "Gus Dur" Wahid with 12.83% of the votes, followed by Vice-President Hamzah Haz's United Development Party (PPP) with 8.31%.
The upstart Democrat Party of Megawati's former security minister Susilo Bambang Yudhoyono was in fifth place with 7.48%. It is seen as having taken the votes of millions of disaffected Megawati supporters.
More than 147 million people
had the right to vote on 5 April
Five other parties reaped more than one million votes, including the Concern for the Nation Functional Party, which is now favoured by the Suharto clan over Golkar. The party supports the presidential candidacy of the patriarch's eldest daughter Siti "Tutut" Hardiyanti Rukmana.
Manoeuvring for the 5 July presidential race - the first direct vote for the country's top position - was already heating up.
With no single party expected to hold a parliamentary majority, building coalitions is vital for the presidential race. Eleven parties have announced the formation of a loose alliance in an attempt to agree on a candidate.
Yudhoyono, a former general whose popularity rocketed after his resignation from Megawati's cabinet in March, was due to meet on Sunday Hidayat Nurwahid, leader of the Prosperous Justice Party (PKS).
Hidayat Nur Wahid's PKS party
made a strong showing
The well-organised Muslim-oriented PKS, which campaigned on an anti-corruption platform, has also made a strong showing, placing sixth with 6.99% of the vote. It leads the polls in Jakarta.
The Reform Star Party, a splinter group of the PPP which only garnered 2.18% of the vote so far, is likely to root for Nurwahid's candidacy, its deputy chairman Zaenal Ma'arif told the Detikcom online news service.
Yudhoyono, speaking to journalists after a Quranic recital at the Istiqlal main mosque also attended by Nurwahid, called on all "not to quickly accuse the General Election Commission as wrong".
Members of 19 political parties on Saturday said they would reject the computerised count of the parliamentary election, alleging that the process organised by the commission was riddled with problems.
Foreign election monitors said the polls were generally fair despite administrative shortcomings.