What happens next could determine whether al-Qaida Central, still in hiding in Pakistan's badlands amid a deadly drone offensive by the United States, will be able to continue functioning.
But at the very least, it reinforces the belief that control of al-Qaida is slipping from the hands of Zawahiri, Osama bin Laden's longtime Egyptian deputy who took over the organization after bin Laden was assassinated by U.S. Navy SEALs in May 2011, as the jihadist movement becomes more diffuse.
The split became apparent on April 8, when the leader of the Islamic State of Iraq, al-Qaida's Iraqi wing, announced in an audio statement his group was controlling Jabhat al-Nusra, or al-Nusra Front, the leading jihadist group fighting the Damascus regime in Syria's 27-month-old civil war.
Abu Bakr al-Baghdadi named the new alliance the Islamic State of Iraq and the Levant, which would make it the largest and most powerful of al-Qaida's affiliates.
His proclamation, which had the appearance of a takeover rather than a mutually agreed merger, apparently took al-Nusra Front leader, Abu Mohammed al-Golani, by surprise.
He declared while ISI had provided his group with valuable support, he had not been consulted on any alliance. He vowed his group would remain independent from ISI, and again pledged his allegiance to Zawahiri.
The problem was after al-Baghdadi's declaration and Golani's rejection, large numbers of al-Nusra fighters defected to join al-Baghdadi organization, the Islamic State in Iraq and the Levant.
In a May 23 letter, Zawahiri rebuked al-Baghdadi for his actions and failure to coordinate with al-Qaida Central, then proclaimed the alliance dissolved.
Al-Baghdadi's power play was "the most dangerous development in the history of global jihad," an al-Nusra spokesman told al-Jazeera June 8.
In a June 14 audio message posted on Islamic websites, al-Baghdadi declared in what appears to be a clear case of insubordination: "The Islamic State of Iraq and the Levant will continue. We will not compromise and we will not give up."
In a direct challenge to Zawahiri's authority and legitimacy, he even called into question the authenticity of the May 23 letter.
"I chose the command of God over the command that runs against it in the letter," al- Baghdadi said.
Zawahiri, apparently anticipating trouble from al-Baghdadi, said in his letter he was sending a veteran al-Qaida operative, Abu Khalid al-Suri, to settle "any dispute" between the two leaders "arising from the interpretation of this ruling."
If necessary, he said, Suri has the authority to set up a Sharia court of justice -- based on Islamic religious law -- "to give a ruling on the case."
There, for now, the matter rests. But this rift not only displays ruptures within the international al-Qaida network, it calls into question the authority and even relevance of al-Qaida Central itself at a time when the global jihad has been decentralizing through regional groups that operate with considerable autonomy.
The roots of this tension go back to 2004, when al-Baghdadi's predecessor, Jordanian Abu Musab al-Zarqawi, who founded al-Qaida in Iraq, was censured by bin Laden and Zawahiri for needlessly killing Muslims, including rival Shiites.
"If al-Baghdadi's revolt goes unchecked, it very well might spell the end of the concept of a global, centrally directed jihad, and it could be the next step in the devolution of the jihadist movement as it becomes even more regionally focused," analyst Scott Stewart of the U.S. global security consultancy Stratfor said.
"Despite the long-standing weakness of the al-Qaida core group, to this point the franchise groups have been careful to publicly maintain a face of paying homage to the core leadership.
Al-Baghdadi's actions could be attributed to the absence of the widely revered bin Laden.
Zawahiri, former leader of Egypt's al-Gamaa al-Islamiya, is prickly and irascible. Many saw him as bin Laden's eminence grise, but he's not held in the nearly same esteem as his predcessor.
Unless Zawahiri can forcibly assert his authority swiftly, he may face challenges in the months ahead since al-Baghdadi appears to have leadership ambitions that go beyond Iraq.