But with a projected total of 55 seats in the new 88-member constituent assembly, Fretilin will be short of the two-thirds majority needed to approve constitutional changes.
Fretilin win
57.3% of the popular vote
12 of 13 district seats
43 of 75 national seats
Carlos Valenzuela, the United Nations chief electoral officer in East Timor, called the vote "the most peaceful election I've ever been involved in, and the most consolidated and democratic election ever held under the auspices of the United Nations".
They follow a 1999 vote for the territory to become independent from Indonesia, which came amid a campaign of violence by pro-Jakarta militias.
Pro-independence past
Fretilin - the Revolutionary Front for an Independent East Timor - spearheaded the fight for independence from Indonesia in East Timor, which was a Portuguese colony before 1975.
Fretilin was formed as a radical left-wing pro-independence party in 1974 at the end of Portuguese rule and before East Timor was invaded by Indonesia.
The territory is under an interim United Nations-run administration until presidential elections and full independence next year. After being sworn in, the assembly has 90 days to ratify and adopt a constitution.
Fretilin won 12 of the 13 seats representing districts and 43 of the 75 national seats allocated by proportional representation.
The Democratic Party came in second place with seven seats. Two other parties won six seats each, while a range of eight smaller parties split the remaining seats.
Concerns
East Timor's leading human rights group, Yayasan Hak, had expressed concern about a large Fretilin majority.
"Fretilin has already prepared a draft constitution. If they have the majority of seats, they could adopt this without consultation," said the group's spokesman Joaquim Fonseca.
The results announced by the UN on Thursday do not give Fretilin a large enough majority to adopt a constitution unilaterally.
The assembly is expected to be sworn in on 15 September.
The UN's chief administrator in East Timor, Sergio Vieira de Mello, will pick the cabinet, which will be answerable to him until full independence in March or April next year.
The former separatist guerrilla leader, Xanana Gusmao, has announced his intention to run for the presidency and is widely tipped to win.
More than 91% of eligible voters turned out for the 30 August poll. The results announced on Thursday were "final provisional results".
Confirmed, certified results will be announced on 10 September.