"Your unprecedented holy war and steadfastness are beyond the limits of my description. It's a divine victory. It is a victory of Islam," Khamenei said in the message read by an announcer on Hizbullah's al-Manar television.
Hizbullah is heavily financed and backed by Iran's Shiite Muslim theocracy.
"Your victory was a victory for Islam. With God's help you were able to prove that military superiority is not (measured) in the number (of soldiers), planes, warships and tanks. Rather, it depends on the power of faith and holy war," Khamenei said.
"You have ridiculed the myth that the Zionist army is invincible," He said.
Khamenei said the Israeli attacks targeting Lebanese civilians and infrastructure and the "massacres" In Qana and other Lebanese villages have exposed "the real face of America and some European countries, side by side with the hated and repugnant Zionist face."
"They (Israeli attacks) have also uncovered the level of falsehood surrounding the hallow slogans propagated by those about human rights and democracy," Khamenei said.
He lashed out at US President George W. Bush for declaring that the Israeli assault in Lebanon was self-defense and had defeated the militant Shiite guerrillas.
"It (Bush's statement) has embodied before the eyes of everyone a flagrant example of this severity, outrage and injustice," Khamenei said.
He is the supreme religious authority to Hizbullah followers.