The Brotherhood, the country's largest opposition group, is officially banned as a political party in Egypt but fielded candidates as independents.
It won 30 seats, while the ruling National Democratic Party (NDP) won 50, the semi-official Middle East News Agency (MENA) reported on Wednesday, quoting judges in counting stations.
However, the NDP's tally is likely to rise, because many of the 45 independents who won on Tuesday are former members of the party who stood alone after failing to win the party's nomination.
Such independents usually rejoin the party at the end of the elections. Other opposition parties and groups scored eight seats, MENA reported.
Doubling the score
The results of Tuesday's runoffs and last week's polling, the first round in the four-week elections, mean the Brotherhood has captured 34 seats in the People's Assembly, more than double the 15 it held in the outgoing assembly.
This confirms its position as the biggest opposition group to President Hosni Mubarak's government.
"The result confirms in an unquestionable way that the Egyptian people stand behind the Brotherhood"
Deputy leader of the Brotherhood
Brotherhood candidates won in six electoral constituencies in Minya, while the ruling party got five out of 22 seats, less than 25% of the seats it got in 2000, Aljazeera's correspondent Omar al-Kahki reported.
The voting for parliament's 444 elected seats is not expected to end the ruling NDP's control of the chamber, but the Brotherhood wins underlined the status of political Islam as the strongest opposition force.
"The result confirms in an unquestionable way that the Egyptian people stand behind the Brotherhood and that the Brotherhood really do represent the strongest social and political group in Egypt," deputy leader of the Brotherhood Mohamed Habib said.
Campaigning under the slogan "Islam is the solution", the Brotherhood aims to bring legislation into line with Islamic laws. It also calls for more political freedom in Egypt, ruled by Mubarak since 1981.
The Brotherhood is fielding about 100 candidates in the second and third rounds of the election on 20 November and 1 December.