Aoun's candidates will run against Druze and Muslim opposition leaders in his Mount Lebanon district.
Since the February assassination of former Prime Minister Rafiq al-Hariri, Druze, Muslim and Christian opponents of Syria's influence in Lebanon have banded together to form a united opposition.
"We've decided to wage the election and the decision will be for the Lebanese," said Aoun on Tuesday.
Aoun and his lieutenants were locked in marathon negotiations that lasted until Tuesday's early hours, between representatives of Druze leader Walid Jumblatt and Saad al-Hariri, son of the slain former prime minister.
The negotiators failed to reach joint tickets in the Mount Lebanon province.
"Therefore, the Lebanese people will be the judge and with this the people will be able to exercise their rights in full," said Aoun, a former army commander who returned from France after 14 years of exile to Lebanon on 7 May.
On returning, Aoun had vowed to use his stature to help build a broad opposition alliance. But opposition figures had been putting together their own election deals that were leaving him out in the cold.
Aoun fought and lost a "war of liberation" against the Syrians in Lebanon in 1989, and now regards himself as the "real opposition" - in contrast to politicians he says were Syria's allies but turned recently on Damascus along with popular sentiment.