"By exploiting inattention ... corrupt American, NATO and Zionist agents are trying to divert the deluge-like movement of Muslim youth and bring them into confrontation with one another in the name of Islam," he said in an annual message to Iranians who have gone to Saudi Arabia for the haj pilgrimage.
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"They are trying to turn the jihad against colonialism and Zionism into blind terrorism in the streets ... so that Muslims shed each other's blood."
Officials in Shi'ite Muslim Iran often describe the "Arab Spring" uprisings as an "Islamic Awakening".
Some of those uprisings have brought Islamists to power, while others, notably in Syria and Bahrain, have pitted Sunnis against Shi'ites or Alawites, members of an offshoot of Shi'ite Islam.
'No intervention in Syria'
Iran has aligned itself with its regional ally Syrian President Bashar Assad and Lebanon's Shi'ite Hezbollah movement in what it calls an "axis of resistance" against Israel. At the same time it denies accusations from Sunni-ruled Gulf monarchies that it is encouraging Shi'ite uprisings in their countries.
"The aggressive and interventionist arrogant powers are making every effort to divert the course of these significant Islamic movements," Khamenei said, according to Iranian state television, urging Muslims to show solidarity.
He reiterated Iran's opposition to outside intervention in Syria, saying only Syrians could decide their own future, and said other unspecified nations could also be engulfed by Syria's turmoil.
On Wednesday, international mediator Lakhdar Brahimi said both the Syrian government and most opposition groups had agreed to the principle of a ceasefire during the three-day Muslim Eid al-Adha holiday, which starts on Friday.
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