The four-stage elections -- held over consecutive weekends -- are the first since Syria withdrew from Lebanon. Sunday's vote took place in Mount Lebanon and the eastern Bekaa Valley.
Before Sunday's election, Aoun split from opposition leader Walid Jumblatt -- with whom he had supported an independence movement, the so-called Cedar Revolution. That movement peaked in March and pressured Syria to remove its troops from Lebanon.
The third round was crucial as it is deciding nearly half of the seats in the parliament.
In the first round of voting, the son of assassinated former Prime Minister Rafik Hariri won all seats up for grabs in the capital of Beirut.
But Syria's most powerful allies in Lebanon, Hezbollah and Amal, won phase two of the elections in the southern areas bordering Israel.
The final round of voting, to be held next Sunday, will take place in northern Lebanon.
Ex-pro-syrian Jumblatt accused Aoun of being brought into the election by the Syrians to undermine the opposition in the third phase.
The Associated Press quoted him as saying. "True he succeeded, I concede that."
The lebanese leader's victory in the third round means he could play a critical role in the debate over Syrian control of Lebanon and whether pro-Syrian President Emile Lahoud retains his position.
"I'm staying to the last moment that I have in my tenure," Lahoud vowed Sunday.
His cousin, Nassib Lahoud, a Lebanese opposition candidate who appeared headed to defeat, said he fears he could be targeted for assassination.
"I think we are all in danger," he told reporters. "There is no reason to feel safe as long as we don't have control of the security services."
Voting was overshadowed by U.S.-backed opposition claims that Syrian intelligence agents are still active in Lebanon.
Syria maintains that all its forces left Lebanon in April following international pressure over the killing of former Prime Minister Hariri and calls the U.S. allegations inaccurate and unfair.
In Washington, the Syrian ambassador to the United States vehemently denied White House Allegations Sunday that Syria is targeting Lebanese politicians and activists for assassination.
Saying it was "a shame" U.S. officials would "degrade" themselves by believing such reports, Imad Moustapha told "Late Edition with Wolf Blitzer" that the allegations, voiced Friday, were analogous to now-disproven U.S. accusations that Iraq was harboring weapons of mass destruction.
Syria "has withdrawn from Lebanon completely," Moustapha said, calling conflicting reports "unbased" and a part of a "sinister campaign against Syria."
Moustapha's defense of his country occurred days after President Bush leveled a stern warning against Syria regarding the "troubling" reports.
"Our message to Syria -- and it's not just the message of the United States, the United Nations has said the same thing -- is that in order for Lebanon to be free, is for Syria to not only remove her military, but to remove intelligence officers as well," Bush said Friday.