He said the victory over the Daesh is tantamount to the defeat of plots to sow division and wage a civil war in the Middle East, adding it is a blow to plots by the US and its allies, Xinhua News Agency reported.
Khamenei's remarks come in response to a senior Iranian Military General, who announced on Tuesday the final defeat of the IS militants in Iraq and Syria and congratulated Iran's Supreme Leader on the "victory."
Major General Qassem Soleimani, Commander of the Quds Force of Iran's Islamic Revolution Guards Corps (IRGC), on Tuesday hailed the "great victory" over the IS.
He said the ultimate victory was achieved thanks to Khamenei's prudent leadership and the sacrifices of all resistance fighters in Iraq and Syria.
Declaring full victory over the "notorious terror group", he said the armed forces in Iraq and Syria, backed by popular groups and Iranian military advisors, have managed to flush the IS militants out of their last strongholds in both countries.
He also praised what he called the steadfastness of the Iraqi and Syrian nations, governments, armies and popular forces throughout the counter-terrorism battles.
Soleimani also expressed his gratitude to Lebanon's Hezbollah Shiite movement for its "powerful presence" and the pivotal role it played on the battlefield against terrorists in Syria.
He said initial reports estimate that the damages caused by the Daesh militants in the two countries amounted to at least $ 500 billion.
Khamenei also warned against what he called the enemy's deceit, adding that those who made a huge investment to create the IS would try to re-hatch their evil plots in another part of the region or in other forms.