"We stand beside you and will seriously defend your government like the previous government," Khamenei said in a meeting in Tehran with Iraq's Prime Minister Haidar al-Abadi.
"Iran recognises the security of Iraq, (our) neighbour and brother country, as its own security," Khamenei said, quoted by state television.
The all-powerful Iranian leader said he believed that Iraqis had "the capacity to overcome the terrorists and establish security" alone without the "need for foreign presence".
But in early October, Iranian television published a rare picture of its elite Quds Force chief, Major General Qassem Suleimani, in an Iraqi battlefield alongside Kurdish peshmerga forces.
And in September, a senior Iranian military official threatened to attack deep inside Iraq if the IS jihadists approached his country's border.
Tehran, which has refused to join the international coalition against IS, advocates regional support for the Iraqi and Syrian governments, and says that air strikes are insufficient.
But at the same time the Iraqi premier appeared to set restrictions on Iran, saying no "regional power will fight here".
Today, during his first official visit to Iran since his appointment last month, Abadi said his country was at war with "terrorists" threatening the region.
"Iraq is not fighting terrorism only. It is an extensive war with all these groups," he said, alluding to IS and other extremist fighters such as Al-Qaeda's Syria affiliate Al-Nusra Front.
"It's a threat to the region and these terrorist groups are trying to create a division between Shiites and Sunnis," the official IRNA news agency quoted him as saying.
The visit was originally scheduled to last one day but will continue tomorrow with Abadi set to meet influential former president Akbar Hashemi Rafsanjani and parliament speaker Ali Larijani.
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