Ayman al-Zawahiri’s ruling came in a letter addressed to the leaders of Syria-based Jabhat al-Nusra and the Islamic State in Iraq (ISI), which is the largest jihadi umbrella group in the country, according to Al Jazeera.
The ruling comes two months after the leader of ISI, Abu Bakr al-Baghdadi, declared a merger with al-Nusra to form the Islamic State of Iraq and the Levant (ISIL), saying that al-Nusra was "merely an extension and part of the Islamic State of Iraq".
However, the unilateral move led to defections, infighting and a breakdown in operations as members disagreed over who commanded the battlefield.
In the letter, Zawahiri said Baghdadi was "wrong" to declare the merger without consulting or even alerting al-Qaeda's leadership.
He added that Syria was the "spatial state" for al-Nusra, headed by Abou Mohammad al-Joulani, while Baghdadi’s rule would be limited to Iraq.
Al-Nusra, listed as a terrorist organization for its affiliation with al-Qaeda, is considered to be one of the most important groups fighting against the government in a massive bloodshed in Syria.
But after Baghdadi released a video in April declaring the formation of the ISIL, many of al-Nusra’s fighters left to join the new umbrella group.
"This was the most dangerous development in the history of global jihad," an al-Nusra source inside Syria told Al Jazeera on Saturday.
One al-Nusra fighter estimated that 70 percent of the group's members left for the ISIL in Idlib province, with even higher defection rates in the Syria’s eastern regions.
Aleppo, the bastion of al-Nusra, saw the least defections from its ranks, terrorist fighters said. But even then the city suffered from the divisions within the group.
The division made the everyday practices of governance and fighting even more challenging.