"I call upon the ulama (Muslim clergy) in Pakistan... Musharraf and his hunting dogs have tarnished your honor in service of the crusaders and the Jews," Zawahiri said in an audiotape posted Thursday on the Internet.
Zawahiri said that he was speaking on the "occasion of the criminal aggression" on the mosque.
"If you do not revolt, Musharraf will annihilate you. Musharraf will not stop until he uproots Islam from Pakistan," he added.
At least 70 gunmen and five soldiers were killed after Pakistan's army launched an attack on the Lal Mosque on Tuesday. Othe sources put the number of deaths as high as 250.
After more than 30 hours of fighting against followers of the gunmen leader Abdul Rashid Ghazi, who died in crossfire on Tuesday night, troops took control of the site mid-Wednesday.