The Freedom and Justice Party won 36.5 per cent of the vote for party lists according to the electoral committee for the second round which was held on 14 December. Al-Nur won 28.78 per cent of the vote.
In Egypt's complex electoral system, voters cast ballots for party list candidates who will make up two thirds of parliament, and direct votes for individual candidates for the remaining third.
The elections were scheduled over three rounds, with run-offs for individual candidates after each round.
Electoral chief Abdel Moez Ibrahim announced the winners for the individual vote, but not their affiliations.
The official Al-Ahram newspaper reported that the FJP won 40 seats and Al-Nur 13.
The Islamists' liberal rivals fared badly again in the second round, with Al-Wafd, the country's oldest party, winning 9.6 per cent of the party list vote and the Egyptian Bloc, the main liberal coalition, just seven per cent.
The third round of the election will start on 3 January followed by another three-round poll for the senate.
The FJP has said it would have the right to form the next government, but the ruling military and the prime minister have said parliament could not appoint ministers.
The military, which has faced down days of deadly protests in November and this month, says it will transfer power to civilians after a presidential election is held by the end of June next year.