Vanunu said he did not want to work in mainly Jewish west Jerusalem for fear that he would be "harassed by the Israeli population".
The court rejected his request and ordered him to serve three months behind bars.
"Shame on you, Israel, and the stupid Shin Bet and Mossad spies who are returning me to jail after 24 years in which I have spoken only the truth," Vanunu shouted in court before being led away, referring to Israel's internal security arm and its international spy service.
"Freedom is a basic part of human rights. I am not an animal. You punished me in the past, but I cannot accept a violation of my freedom of expression."
Vanunu was jailed in 1986 for disclosing the inner workings of Israel's Dimona nuclear plant to Britain's Sunday Times newspaper.
Since his release in 2004, he has been detained several times for violating the terms of his release that ban him from travel or contact with foreigners.
Israel has restricted his movements and personal contacts since he finished his first jail term.
Israeli authorities argue that Vanunu could leak new details on his past work at the Dimona nuclear reactor.
But Vanunu, a convert from Judaism to Christianity, denies charges that he has more classified information that he can leak if he is allowed to emigrate.
Israel is widely believed to be the only nuclear-armed power in the Middle East, with around 200 warheads, but it has a policy of neither confirming nor denying that.
It has refused to sign the nuclear Non-Proliferation Treaty or to allow international surveillance of Dimona in the southern Negev desert.