Khamenei accuses Lebanon, Iraq revolutionaries of being 'Zionist' tools
"The people of Iraq and Lebanon have some demands that are rightful, but they should know these demands can only be realised within the legal framework of their countries," he said in remarks aired on state television.
"When the legal structure is disrupted in a country, no action can be taken," he added.
He also took to his English Twitter account to repeat his claim that has been lambasted as a conspiracy.
"I recommend those who care in #Iraq and #Lebanon remedy the insecurity and turmoil created in their countries by the U.S., the Zionist regime, some western countries,and the money of some reactionary countries", he said in a controversial tweet.
Iran's President Hassan Rouhani echoed Khamenei, accusing those protesting against corruption of "foreign interference".
"Our advice has always been to call for peace and (stopping) interference by foreign forces in these countries,” President Hassan Rouhani's chief of staff Mahmoud Vaezi was quoted as saying by state media.
Both comments were met with anger across the Arab world, with protestsers accusing Iran of using its geopolitical muscle as a way of undermining popular calls for greater rights and freedoms in Iraq and Lebanon, where Tehran has huge influence through militias.
On Friday, clashes erupted when partisans of the powerful Iranian-backed Shia group entered Beirut's Riad Al-Solh square, chanting in support of Hezbollah.
On Monday, pro-Amal and Hezbollah supporters also rampaged through a protest camp in the same site.
The rallies in Iraq and Lebanon ignited hopes of a renewal of the Arab Spring in the two countries both plagued by corruption, mismanagement, and a power structure based on sectarian affiliation.
Earlier this year, protests also broke out in Algeria and Sudan, prompting the departure of longtime dictators Omar Al-Bashir and Abdelaziz Bouteflika.
One major difference between the protests in Lebanon is the level of force the authorities are willing to use.
While protesters in Lebanon have clashed with the army and been attacked by supporters of the Hezbollah and Amal movements, who both participate in government, there have been no fatalities.
By contrast, over 250 protesters have been killed in Iraq since protests began on 1 October, and security forces have used machine guns against protesters as well as tear gas.