The interview, which the SITE monitoring service dated to between February and April, was released after the Islamic State of Iraq and the Levant (ISIL) accused Al-Qaeda of having "deviated from the correct path."
"They have divided the ranks of the mujahideen (holy warriors) in every place," ISIL spokesman Abu Mohammed al-Adnani said in a statement posted on jihadi forums.
Zawahiri rejected the allegations, suggesting that Syrian President Bashar al-Assad's regime may have penetrated jihadist groups in order to sow sedition, according to SITE, which translated his interview with a Qaeda-run media outlet.
The split dates back to last year, when Zawahiri ordered ISIL to confine its activities to Iraq after it was accused of widespread abuses against Syrian civilians and rival rebels.
Zawahiri, who succeeded the late Osama bin Laden as leader of the global terror network in 2011, declared Al-Nusra Front to be the official Al-Qaeda affiliate in Syria.
"Our method is to focus on the Hubal (pre-Islamic pagan god) of the era, America, and its Crusader allies and the Zionists and their traitor agents, and to incite the Ummah (Muslim community) and rally it for jihad against them and leaving the side skirmishes," Zawahiri said in the interview.
Syrian rebels initially welcomed battle-hardened jihadists to their struggle, but Islamist and non-Islamist groups alike turned on ISIL after it began kidnapping, torturing and killing activists and rival rebels, and imposing its strict version of Islam by force.
Syria's uprising began with peaceful protests in March 2011 but escalated into an insurgency and then a civil war after the regime launched a brutal crackdown on dissent. More than 150,000 people have been killed since the revolt began.
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