And while senior leaders of Al-Qaeda were all but above question under revered founder Osama bin Laden, the conflict has gone so far that even his replacement Ayman al-Zawahiri has come in for fierce criticism on jihadist forums online.
Powerful rebel groups in Syria, including Al-Qaeda's designated local affiliate Al-Nusra Front, have been locked in fierce fighting with jihadist group the Islamic State of Iraq and the Levant (ISIL), with thousands of people killed since January.
Jihadists were initially welcomed by other rebels battling to topple Assad since 2011.
But allegations of brutal abuses against civilians and rival fighters sparked a backlash and even accusations that they served Assad's interests.
In a sign of how sharp the divisions have become, ISIL spokesman Abu Mohammed al-Adnani has accused Al-Qaeda leaders of betraying the jihadist cause.
"Al-Qaeda today is no longer a base of jihad (holy war)," Adnani said in a statement posted on jihadist forums, playing off the militant group's name, which means "the base" in Arabic.
"Its leadership has become a hammer to break the project of the Islamic State," Adnani said, adding that "the leaders of Al-Qaeda have deviated from the correct path".
"They have divided the ranks of the mujahedeen (holy warriors) in every place."
- Zawahiri under fire -
Online, the clash among jihadists has seen criticism of Zawahiri from around the Islamic world, though others have defended the Al-Qaeda chief.
"Zawahiri has fallen... We will not listen to him any more. To the dustbin of history, oh Al-Qaeda," tweeted ISIL supporter Munassar al-Mumineen.
Ahmed, another Twitter user, attacked Zawahiri as "old" and called him "the Prince of the Khawarij" -- those who have left the proper path of jihad.
Charles Lister, a visiting fellow at the Brookings Doha Centre, said the dispute is ultimately over leadership of the jihadist movement.
"This division has become more about the fight to represent the true jihadist movement, both in Syria but also internationally," Lister said.
"This continuing battle for influence between Al-Nusra and ISIL has the potential to cause shock waves across the international jihadist community.
"The conflict in Syria has provided an enormous opportunity for jihadist groups, and with such a significant opportunity comes the possibility of divisions," he added.
Alan Fraser, a Middle East and North Africa specialist with British risk consultancy AKE Group, said disputes among jihadists have happened before, including within Al-Qaeda itself.
"Jihadist groups have always been prone to division and infighting, as there is generally a lot more at stake than just ideological issues," he said.
"There have always been tensions between and within groups over the extent of their extremism and the lengths they will go to seek funding and to impose their beliefs on local populations," Fraser said.
"The various schisms that took place within and between Islamist groups in Algeria during and after the civil war is a perfect example of this," he said, adding that "even within Al-Qaeda, there are significant internal disagreements".
- 'Doing Assad's job' -
Inside Syria, splits between jihadist groups ultimately play into Assad's hands.
"Divisions within and between jihadist groups (have) had a major shaping effect on the conflict in Syria," Fraser said.
"It has played a significant role in dividing the opposition movement, as well as dividing opinion and the degree of support among those who had previously supported the uprising."
Over the past year, the Syrian army, backed by Lebanese militant group Hezbollah, has achieved a series of victories, while rebel groups continue to suffer from a lack of supplies, the absence of a unified command structure and infighting.
Lina Khatib, director of the Carnegie Middle East Centre in Beirut, also said inter-jihadist conflict has harmed the rebel cause.
"Divisions have diverted certain groups' energies away from fighting the Assad regime, as is the case of Al-Nusra Front, which today is deeply involved in confrontations" with ISIL, Khatib said.
"The Assad regime is benefiting from infighting among jihadist groups, as they are doing the job for Assad."