Despite tight security, correspondents say many voters in the capital, Brazzaville, were afraid to venture out after recent clashes between government troops and rebels opposed to President Denis Sassou-Nguesso.
Voting remained postponed in eight constituencies in the southern Pool region of Congo-Brazzaville, where fighting marred the first round earlier in the month and nearly 50,000 people are displaced.
The new 137-seat single chamber parliament will replace a transitional body under a constitution approved last January.
In the first round, only 51 of the seats were determined, with the party of President Sassou Nguesso winning 29 of them.
Opposition scepticism
The main opposition coalition said that the government had decided the results in advance.
"This risks ending up as a rubber-stamp parliament," said Andre Milongo of the Union for Democracy and the Republic.
One factor contributing to a low turnout was the more stringent requirements for voter idenitification.
In the first round, people only to show special voter cards to cast a ballot.
But on Sunday, national identity cards, driving licences or passports were required.
"For the second round, I haven't been to vote because I don't have a national identity card," said 32-year-old Brazzaville teacher Clementine Mabiala.
Other residents said that the poll was irrelevant, given the current security situation.
"My house was burned down by (rebels). Who is going to compensate me? Nobody, so why should I bother going to vote?" said 56-year-old retiree Norbert Mbani.
"Why vote if it's always the same ones who come back?" said Luc Mbila, 27.
Disqualified
After the first round, several candidates were disqualified for misdemeanours varying from assault to tampering with voting material.
They included the current minister of finance and President Sassou Nguesso's elder brother.
Once elected, Congo's new law makers will sit in the country's first democratically elected assembly in ten years, though critics say the president will retain most of his powers.
The former military ruler was himself elected earlier this year, winning almost 90% of the vote after opposition candidates either withdrew or were banned from entering the country.