It was not clear when the videotape was recorded but its release comes as tensions are rising in the Palestinian territories after small-scale clashes and a call by Mahmoud Abbas, the Palestinian president, for early elections.
Walid Batrawi, an Al Jazeera correspondent in Ramallah, said: "It's very hard to predict the effects of the message. It comes at a very sensitive time."
"Any road other than jihad will only lead to loss"
Al-Zawahiri said: "Accepting the legitimacy of Mahmoud Abbas, the head of the national authority, America's man in Palestine, and mandating the PLO which recognises Israel to negotiate with Israel is an abyss which will ultimately lead to eliminating the jihad and recognising Israel."
In a previous video, marking the fifth anniversary of the attacks on the US of September 11, 2001, al-Zawahiri said that the Gulf and Israel would be al-Qaeda's next targets.
Egyptian-born al-Zawahiri carries a $25m US bounty for information leading to his arrest or death.