The tape, aired on al-Jazeera today, appears to confirm a letter put out by al-Jazeera in June, claimed to have been written by Zawahiri and addressed to the leaders of al-Qaeda factions in both countries.
The head of al-Qaeda also stressed that the al-Nusra Front was the branch of the global jihadist group in Syria.
"The Islamic State in Iraq and the Levant (ISIL) is to be abolished, while the Islamic State of Iraq (ISI) remains functioning," he said.
It was not immediately clear when he made the remarks.
Meanwhile, Zawahiri added that the leader of the Al-Nusra Front in Syria, Abu Mohammad al-Jawlani, "has made a mistake by announcing his rejection of the ISIL, without taking our permission, or even informing us."
He said the rule of ISI will be confined to Iraq, while the al-Nusra Front in Syria will be "an independent branch of al-Qaeda that reports to the general command."
Opposition activists have blamed the ISIL for an escalating abuse against Syrian rebels and civilians, including kidnappings and public executions in areas under the control of the extremist group.
Zawahiri chided Islamists from both sides for unauthorised attacks on Muslims.
"Both sides, and all the mujahedeen (Islamist fighters) should observe the sanctity of Muslims, in respecting their blood, families and property, and should not attack a Muslim without a court order," he said.
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