According to results announced by Interior Minister Hassan al-Sabei on Monday, Aoun and his allies clinched a total of 21 of the 58 seats contested on Sunday, at least temporarily thwarting the opposition's quest for a majority in their drive to end Syria's political control.
Meanwhile, the Shia Muslim Hezb Allah resistance group and its allies swept 10 seats in the eastern Bekaa Valley while Druze leader Walid Jumblatt's list won in central Mount Lebanon.
Aoun's success dealt a major blow to the Christian opposition and its hopes of securing strong representation in the new 128-seat parliament and charting a course away from Syrian influence.
The polls, being held over four weekends ending on 19 June, are the first without the presence of Syrian troops for three decades and are set to usher in an assembly with an anti-Syrian majority for the first time since the 1975-1990 civil war.
Aoun's victory could complicate the new political landscape in highly factionalised Lebanon as it boosts the chances of pro-Syrian President Emile Lahoud staying in power.
Aoun has questioned opposition demands for Lahoud to go.
"General Michel Aoun has established an influence on the Christian arena unmatched" by any other political leader or party since the civil war, said the As-Safir newspaper.
Aoun, who launched a failed "war of liberation" against Syrian forces in Lebanon in 1989, was forced into exile in France after the Syrians crushed his revolt in 1990.
Aoun's supporters say he is untainted by years of corruption among Lebanese politicians while Syria held sway after the civil war and accuse rivals of trying to contain his influence.
He fell out with other anti-Syrian leaders after returning.
"I believe it is a victory because all political forces sided together against us," said Aoun, vowing to fight corruption that he blames for Lebanon's economic problems.
"We are back to 1976 when the Syrians entered Lebanon with the pretext of protecting the Christians, but their first and last intention was to control Lebanon"
Druze leader Walid Jumblatt
In the Baabda-Aley district, where 11 seats were contested, Aoun-backed candidates narrowly lost to opponents supported by Druze leader Walid Jumblatt.
Jumblatt, whose candidates won all eight seats in his mainly Druze stronghold of Shouf, said Aoun's victory was a defeat for moderation, and accused him of being used by Syria and its Lebanese allies to divide and weaken the Christians.
"We are back to 1976 when the Syrians entered Lebanon with the pretext of protecting the Christians, but their first and last intention was to control Lebanon," he said.
Resistance group Hizb Allah and its allies increased their share in parliament, with 10 candidates winning seats in the eastern Baalbek-Hermel district.
The alliance now has 35 seats in the assembly.
The son of slain former prime minister Rafiq al-Hariri suffered a setback in Zahle, a mainly Christian constituency in the eastern Bekaa Valley, where he has no traditional base.
But candidates backed by Saad al-Hariri won all six seats in a mainly Sunni Bekaa constituency.