The message purportedly from Zawahiri, carried on al-Shabaab's website, called for a campaign of guerrilla warfare against the African troops fighting the militants, the Voice of America reported.
VOA said the speaker, talking in Arabic, mentioned Kismayo, a port from where the al-Quaida-allied militants were driven out last month by the Kenyan unit of the African forces which are supporting the Somali government. The mention of Kismayo indicated Zawahiri's message was recorded recently, the report said.
The message asked the jihadists to ambush the foreign troops or resort to suicide bombings against them regardless of their numbers.
The Kismayo defeat was the latest for al-Shabaab in the hands of the African forces from Kenya, Ethiopia and the African Union. The militants had earlier been in control of much of the country, which has suffered anarchy for more than two decades.