The remarks were greeted by chants of "Death to America" at a ceremony in Tehran marking the end of the Muslim fasting month of Ramadan, which was broadcast live on state television.
Khamenei also said Tuesday's nuclear agreement would not alter Iran's support for the governments of Syria and Iraq nor its backing of "oppressed people" in Yemen and Bahrain, and the Palestinians.
The comments reflected the supreme leader's longstanding position that Iran's engagement with the six powers was solely to reach a nuclear deal that was in its national interest.
In return, Iran has pledged to place curbs on its nuclear programme for at least a decade to assuage western concerns that the Islamic republic has sought to develop an atomic bomb.
Iran has always denied seeking a nuclear weapon, insisting its atomic programme is for peaceful energy and medical purposes only.
Khamenei restated that position today, mentioning a fatwa he himself issued against any action seeking the bomb.
He also stressed that the agreement with Britain, China, France, Russia and the United States plus Germany was not yet law and would have to be carefully scrutinised.
"They really took pains and worked hard," Khamenei said of the team led by Foreign Minister Mohammad Javad Zarif.
"The text that has been prepared, whether it is approved or not, they have done their part and they should have their reward," he added.
As Iran's supreme leader, Khamenei has the final word on all policy matters, foreign and domestic, including on the nuclear deal.
In numerous speeches before this week's accord, he appeared ambiguous about the talks, consistently talking down the chances of success but at the same time hailing Iran's negotiators as trustworthy and brave.
The SNSC is headed by Rouhani and the powerful committee reports directly to Khamenei.
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