The recording follows a statement released this month by al-Zawahiri that said al Qaeda in Iraq and al-Nusra will operate as separate entities with separate leadership.
It's unclear what al-Baghdadi's statement means for al-Nusra's operation in Syria.
Meanwhile, rebel and government forces once again clashed at hotspots around Syria on Saturday, with the opposition Local Coordination Committees of Syria reporting 79 dead. Twenty-four of those deaths were in and around Damascus, 17 were in Aleppo province and 12 were in Homs.
The rebel army has suffered a number of setbacks in recent weeks that in large part have coincided with the arrival of thousands of Hezbollah Shiite fighters, backed by Lebanon and Iran, to reinforce al-Assad's forces.
After months of gaining ground, the rebels this month lost Qusayr -- one of its strongholds near the Lebanese border -- that was considered essential for its supply route.
Syrian forces and Hezbollah fighters have now turned their focus on retaking Aleppo.
Black flag over mosque draws scrutiny
On Friday, Hezbollah leader Hassan Nasrallah criticized Arab networks Al-Arabiya and Al Jazeera for their portrayal of Hezbollah's involvement in the takeover of the strategically important border city of Qusayr, Syria.
When Qusayr fell, a video surfaced online showing Hezbollah fighters raising their black banner over a mosque in Qusayr. A sectarian dispute has arisen over whether the mosque was Sunni or Shiite. Hezbollah is the powerful Lebanese Shiite militia backed by Iran and the Syrian government.
In a Friday speech, Nasrallah defended fellow fighters.
"Yes, there were some young men in Qusayr who, yes, I have to admit -- and there is a room to discuss whether this was right or wrong -- the young men may have gotten too excited and overwhelmed by the events when they climbed to the top of a mosque and raised a black flag that had the writing of O Hussein on it," Nasrallah said.
"The video was then posted online and Arab TV networks like Al-Arabiya, and Al Jazeera grabbed the video and distorted the facts by saying that Hezbollah fighters raised the flag on a Sunni mosque under the pretext that they want their audience to know more. Know what? They are feeding their audience lies, distortions, fabrications," Nasrallah said.
Shortly after Nasrallah's speech, Lebanon's National News Agency reported that "five rockets fired from the Syrian side of the borders landed in Baalbek city in the Kayyal area that were later followed by four other rockets injuring two Lebanese citizens."
The Kayyal area is predominantly Shiite.
Earlier, the Syrian Observatory for Human Rights reported that Syrian rebels in Aleppo fired five rockets at Fawaa village in Idlib, which is mostly inhabited by Shiites, and the rebels said in a statement that the shelling on the Shiite village was a response to Nasrallah's speech.
The human rights group couldn't say whether the rockets landed in the town or whether there were any casualties.