"We do not see the authenticity of the establishment of such a Caliphate, nor what follows it of consequences," al-Nadhari said in a 28-minute video released by Yemen's AQAP today.
He said the fracture among the two most lethal Islamist terror organizations is better than them joining forces against the West.
"Al Qaeda and the Islamic State [ISIS] are still potent in their own right. But they really are at odds with each other," Olsen said.
The AQAP message likely was approved by Nasir al-Wuhayshi, its top leader and Zawahiri's potential heir to core al Qaeda. It came as a response to al-Baghdadi's latest audio speech on Nov. 13, in which he boasted of the pledges of loyalty from a slew of jihadi groups.
"It's further proof that al Qaeda and the Islamic State don't work together," said Rita Katz, director of the private research firm SITE Intelligence Group, who provided a translation of the al-Nadhari speech. She said jihadis reacted angrily to the AQAP message.
"It is important that it came from one of AQAP's top Shariah officials, al-Nadhari, as the argument about the legitimacy of the Caliphate is a religious one. It is more appropriate that such rejection comes from al-Nadhari, a recognized Shariah scholar, and not from Wuhayshi," Katz told ABC News.
"Aside from keeping Wuhayshi above the fray, having their top Shariah official make the statement is also likely a way to highlight the fact that most serious jihadi scholars have come down firmly against ISIS," added terrorism expert J.M. Berger, co-author of a forthcoming book on ISIS's rise.
The announcement comes after months of anticipation after ISIS swept across Iraq in a blitz that caught the Obama administration off guard.
For months, AQAP's messages on Iraq and Syria have avoided taking sides, as many Yemeni fighters joined the estimated 16,000 foreign jihadis who have fallen in with ISIS in the region between Iraq and Syria they call "al Sham." Instead, the Yemeni terror group -- which has attempted at least four air attacks on the U.S. homeland since 2009 using undetectable bombs smuggled aboard passenger and cargo jets -- had repeatedly called on mujahideen fighters there to end their bloody infighting and focus on America and its "apostate" allies.
"We hold our brothers in the Islamic State responsible for all the consequences of these interpretations and dangerous steps [and] weakening the strength of the mujahideen, which is an inevitable result of fighting," AQAP's al-Nadhari said in the message on Friday.