Khamenei referred to Iran's missile strike on the US bases, saying that "they were slapped" on the face.
However, "military operations of this kind is not enough," and "what is important is to put an end to the corruptive presence of the Americans in the region," he said, Xinhua news agency reported.
He gave a speech in Iran's religious city of Qom that was broadcast live on state TV.
Khamenei said that "Americans have brought war, sedition, destruction and division to the region".
He said "our region and the nations of our region no longer accept the presence of Americans."
On Wednesday, Khamenei highly praised "bravery" of General Qassem Soleimani in fighting what he called against the US and Israel "atrocities" vis-a-vis the regional nations.
Soleimani, the former commander of Quds Force of the Islamic Revolution Guards Corps (IRGC), was assassinated in a US airstrike near Baghdad international airport on Friday.
In the early hours of Wednesday, the Islamic Revolution Guards Corps (IRGC) launched the heavy ballistic missile attacks on the Ain al-Asad base near the border with Syria and a US operated airbase in Erbil, reports the semi-official FARS News Agency.
Ain al-Asad has a 4 km runway at 188m altitude from sea levels, which is the main and the largest US airbase in Iraq.
All flights have been cancelled at Erbil airport.
Iraq said the attacks have not taken any toll from its army men stationed at these two bases.
Following the attack, the US army had blocked entrance into Ain al-Asad to everyone, including the Iraqi army.
( With inputs from IANS )