The re-run means 16 seats will not be be declared until April 19, along with another 29 that are distributed on a proportional representation system.
The UPFA's closest rival, the United National Party (UNP), has won 46 seats.
Another opposition party led by Sarath Fonseka, the defeated presidential candidate and former army chief, has received five seats, with Fonseka himself one of those to be elected.
The UNP's spokesman has complained of irregularities in the vote.
"We are not challenging the legality of those who are elected," Tissa Attanayake told reporters.
"But we must stress that there were serious violations in the run-up to the elections ... There was election violence and malpractice on a large scale.
The election result consolidates the political dominance of Rajapaksa, who won January's presidential election.
But it remained unclear if his coalition can secure the two-thirds majority needed to change the constitution.
Opponents have said Rajapaksa might seek a change that would allow him to stand for office beyond the current two terms allowed.
Sri Lanka's opposition has been weakened and fragmented after the arrest of Fonseka, who split with the president after the government's victory over the separatist Tamil Tigers in the country's north.
Held in military custody on charges of sedition, Fonseka has run his campaign for a parliamentary seat while in detention.
The opposition accuses Rajapaksa of stifling dissent, encouraging cronyism and corruption and trying to establish up a family dynasty, with two of his brothers and a son running for parliament and other relatives occupying senior government posts.
Nimalka Fernando, a human rights campaigner and political analyst, said the low turnout in the parliamentary poll would undermine the new government's position.
"The result does not give moral authority to the government because half of the electorate did not vote," Fernando said.
"With the legitimacy undermined, the government will not be able to go for any sweeping reforms."