The Liberal party was third with 14.4 per cent, the Democratic party came fourth with 12.5 per cent, while Our Moldova Alliance received 7.4 per cent of the vote.
If a deal can be reached between the four opposition parties a government could be formed.
Filat said: "We will find the necessary compromise and find agreement so that Moldova finally gets democratic rule.
"Democracy and truth has finally been victorious ... we fought for this for so long and with so many difficulties."
Serafim Urechean, the head of the Our Moldova Alliance, said: "In a short time we will find a favourable solution to develop democracy in Moldova.''
However, Marian Lupu, the Democratic party leader, is a former Communist and if his party were to join his former allies then it could give them enough seats to elect a new president.
Lupu has ruled out any alliance with the Communists unless Vladimir Voronin, Moldova's president since 2001, agrees to leave politics.
Voronin, who has served his two terms as president but made it clear he wants to retain some political position, called the elections in June, after politicians failed to elect a new president due to a boycott by the opposition parties.
Elections in the former Soviet state in April, in which the Communists won about 50 per cent of the vote, triggered huge street protests and riots, which left at least two people dead.
Speaking as the results began to come in on Wednesday night, Voronin hailed the fact that this election appeared to have been conducted relatively peacefully.
"This is the most important thing for us in power," he said. "This is the most important achievement - that we were able to organise civilised and democratic elections."
About 3,000 foreign and Moldovan observers monitored Wednesday's vote, in which about 59 per cent of eligible voters took part.