The Jerusalem Magistrates' Court handed out the sentence after finding him guilty in April of violating restrictions by having contacts with foreign reporters and trying to leave Jerusalem to visit Bethlehem in the West Bank.
Besides a six-month prison term, Vanunu was handed a six-month suspended sentence, a justice ministry spokesman said.
"Although he violated restrictions imposed on him 14 times, the court decided to be lenient and sentence him only to six months in prison," said the court. Vanunu could have faced a maximum sentence of seven years.
"The accused said he considered (the restrictions) illegal," the court found.
The former technician has made repeated appeals to the supreme court to lift the restrictions, which are renewable every 12 months, on his freedom of movement, going abroad and speaking to foreign journalists without permission.
The interior ministry opposes any concessions on the grounds he could leak yet more secrets from his time as an employee at the Dimona nuclear reactor should he be allowed to leave the country.
Vanunu served 18 years in jail for lifting the lid on the inner workings of Israel's Dimona nuclear plant to Britain's Sunday Times newspaper.
He became something of an international cause celebre during his time in prison. At home, he is still widely reviled for converting to Christianity shortly before he was kidnapped in Italy and jailed in 1986 after being covertly shipped back to the Jewish state.
Israel is widely believed to be the only nuclear power in the Middle East with around 200 nuclear warheads but has a policy of neither confirming nor denying its arsenal.
The Jewish state has refused to sign the nuclear Non-Proliferation Treaty or allow international surveillance of Dimona, in the southern Negev desert.