Mullah Akhtar Mansoor takes charge as the Islamic State (IS) group makes gradual inroads into Afghanistan, challenging the Taliban on their home turf.
Zawahiri's declaration on Thursday came with al Qaeda also facing a growing rivalry for global preeminence with IS, which has seized control of large parts of Syria and Iraq.
Read: Countering Islamic State: Al Qaeda's Zawahiri pledges allegiance to new Taliban chief
“I... accept the pledge of allegiance of the esteemed (Zawahiri)... and thank him for... his pledge and pledge of all mujahideen under him,” Mansour said in a statement Friday.
Mansoor was announced as the new Taliban chief on July 31, after the movement confirmed the death of Mullah Omar, who led the group for some two decades.
But splits immediately emerged in the Taliban following the appointment, with some top leaders including Omar's son and brother, refusing to pledge allegiance to Mansoor.
The Taliban have suffered a string of recent defections to IS, which has been trying to establish itself in the eastern regions of the country.
Read: Upping the ante: Kabul to seek action against Afghan Taliban
The recent confirmation of Mullah Omar's death and the growing internal divisions within the Taliban could spur an increase in such defections, analysts say.
The Taliban have repeatedly warned IS against expanding its operations in Afghanistan.
And in a sign of growing rivalry between the groups, the Taliban on Wednesday condemned a "horrific" video that appears to show IS fighters blowing up bound and blindfolded Afghan prisoners with explosives.
The video described the prisoners as "apostates aligned with the Taliban or the Afghan government. But the Taliban said they were "innocent civilians".
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