Aoun returned from exile in Paris and put up a credible showing in last month's parliamentary elections.
The charges stemmed from testimony that Aoun, a Maronite Christian former Lebanese army commander and interim prime minister, made before the US Congress during hearings in 2003.
Those hearings led to accusations by Congress that Syria was abetting terrorism.
Lebanon's government - at the time dominated by Syria - charged the exiled Aoun with actions and comments that "harm Lebanon's relations with a brotherly country (Syria) and spreading false reports that aim to weaken the state's prestige and standing".
But judge Michel Abou Arraj said in his ruling on Tuesday that there was not enough evidence to substantiate the charges.
Return from exile
The charges were the last facing Aoun, who was able to return from exile in May after Syrian forces withdrew from Lebanon the previous month, ending 29 years of military presence and undermining Damascus' domination of its smaller neighbour.
Aoun went into exile in France in 1991 in the aftermath of losing a war against Syrian forces in 1990 in the last battle of the 1975-90 civil war.
He was able to return after other charges that had long prevented his return were dropped. Those charges related to alleged crimes committed before his exile, including usurping power - referring to his refusal to hand over power to an elected president in 1989 after serving one year as interim prime minister.
In the four-stage June elections, Aoun's Free Patriotic Movement won 14 seats in the 128-member parliament, securing Aoun parliamentary immunity and making him a powerful player in the country's politics.