Khamenei made his call as he welcomed the visiting Iraqi President Jalal Talabani on Tuesday.
Khamenei also argued it was the US that was to blame for the ongoing violence in Iraq, amid efforts by Talabani to win Iranian help in tackling the security situation.
"The Islamic Republic of Iran holds the American government responsible for the suffering of the Iraqi people and all the crimes and assassinations now being committed in Iraq," Khamenei was quoted as saying by official media.
"The presence of foreign troops is damaging for the Iraqis, and the Iraqi government could ask for their departure by proposing a timetable," Khamenei said, adding: "The US and Britain will eventually have to leave Iraq with a bitter experience."
Khamenei told Talabani, the first Iraqi head of state to visit Iran in nearly four decades, his country "would be empowered by the development, security, independence and the empowerment of Iraq".
Ties between Iran and Iraq's new authorities have been close, with Baghdad's new government dominated by Iranian-backed Kurdish figures such as Talabani and Shia parties that were backed by Tehran during Saddam Hussein's rule.
Iraqi political analyst Awni al-Qalamchi has said the Iranian statements are designed to tell the US that Iran is a key player in Iraqi politics.
"Iran helped the US occupying Iraq, just like other Arab countries, hoping to benefit politically and financially," he told Aljazeera.net.
Iran-backed Shia have dominated
Iraqi politics since the invasion
"It gained great influence in Iraq when all the political parties it backs ascended to power.
"But when the US realised Iran had become more influential than it should be, it tried to put limits to it.
"Khamenei's statements aim to tell the Americans that Iran is still there and can cause you a headache in Iraq.
"I think Khamenei's statement does not reflect Iran's real position and ambitions in Iraq."
Despite Talabani's statements denying Iran's involvement in Iraq's internal issues, the visit is seen as an attempt to put more pressure on Tehran, whose relations with the US have come to a standstill because of Iran's nuclear ambitions.
Talabani and Iran President Mahmoud Ahmadinejad denied in joint statements the US-UK accusation that Iran is interfering in Iraq's internal affairs.
Talabani said he was confident Iran would provide Iraq with essential help in combatting "terrorism in Iraq".
"The Islamic Republic of Iran holds the American government responsible for the suffering of the Iraqi people and all the crimes and assassinations now being committed in Iraq"
Iran's spiritual leader
"Iraq's President Jalal Talabani does not enjoy the freedom to make his own decisions. We all know that he cannot make any move without US approval," Iraqi political analyst Fadil al-Rubei told Aljazeera.net.
"What is the secret behind promoting Iran's innocence from the US's accusations? I believe that it is a deal.
"The US will help polishing Iran's stained image among Iraqis, in return Iran would send its murderers and killing squads to fight the Iraqi resistance in Falluja and other western Iraqi cities," he said.
Ali al-Awsie, a member of the ruling Supreme Council for Islamic Revolution in Iraq (SCIRI), hailed Khamenei's statement, stressing it reflected the hopes of every Iraqi.
"Khamenei's statements come after the Iraqi national reconciliation conference in Cairo, where all Iraqi factions agreed on asking the US occupation for a withdrawal timetable," he told Aljazeera.net.
But the Iranian-backed SCIRI and other ruling parties in Iraq do not want foreign troops to leave before powerful and effective Iraqi forces are deployed.
"We seek effective guarantees that the situation will be properly maintained after the occupation troops are gone," al-Awsie said.
Aljazeera.net's Ahmed Janabi contributed to this report.