"There is no justification for Iran's case to remain at the UN Security Council," state media quoted Khamenei as telling ElBaradei.
The UN Security Council has so far imposed two rounds of sanctions on Tehran.
ElBaradei met Khamenei and other Iranian leaders during a two-day visit to Tehran to push for more co-operation in resolving questions about Iran's atomic activity.
His visit coincides with renewed Iranian-US tension over a naval incident in the Gulf last Sunday. Washington says its ships were threatened by Iran, Tehran calls it a routine contact.
George Bush, the US president, is also visiting the Middle East this week to seek Arab support in reining in Iran and has repeated his assertion that Iran was a "threat to world peace".
Washington is pushing for a third set of sanctions on Iran for refusing to halt uranium enrichment work, as demanded by the United Nations. Iran says it wants to master enrichment technology so that it can make fuel to generate electricity.
It was not immediately clear what, if any, concrete results were achieved during ElBaradei's first trip to Iran since 2006.
"Americans are mistaken by thinking that by pressuring Iran over the nuclear issue they can break Iran"
Ayatollah Ali Khamenei, Iran's supreme leader,
The IAEA chief told reporters on Friday he was looking forward to "accelerated co-operation" from Iran.
The official IRNA news agency quoted him as telling Khamenei on Saturday: "In recent months there has been good co-operation between Iran and the agency to clarify Iran's activities."
Khamenei was defiant in his meeting with ElBaradei, who is seeking to defuse a standoff that has helped send oil prices to record levels and sparked fears of a military confrontation.
"America's problem with Iran is beyond the nuclear issue," state television quoted Khamenei as saying.
"Americans are mistaken by thinking that by pressuring Iran over the nuclear issue they can break Iran. By bringing this and other issues to the fore, they cannot bring the Iranian nation to its knees."
The IAEA has sought to verify that Iran's uranium enrichment programme is geared solely to producing civilian energy.
Khamenei said that "building or using nuclear weapons is against" Islamic law.
A diplomat close to the IAEA said before ElBaradei's visit that an agency inquiry stonewalled by Iran for years until August had entered a final phase with Iran addressing US intelligence about past attempts to "weaponise" atomic material.
Iran said in August it would answer outstanding questions about its nuclear past but an end-of-year target for completing the process passed with the sensitive issues still unresolved.