Also in the flashpoint city, Israeli police said a woman acting suspiciously and allegedly in possession of a knife was arrested.
Soldiers entered the offices of Al-Khalil radio overnight and handed the station a six-month order to close, said Ezz Haddad, its head of programming.
"Al-Khalil radio station has repeatedly broadcast content which promotes and encourages terror and acts of violence against Israeli civilians and security forces," the army said in a statement.
The station's Facebook page posted pictures of heavily armed Israeli forces arriving at the offices and of alleged damage.
"They took the computers, the communication equipment, everything," Haddad told AFP.
The station was offline on Saturday morning.
Israel's civil administration, a unit of the defence ministry, said Al-Khalil had broadcast "lies about Palestinians being executed and abducted by security forces".
It also cited calls to "stab a soldier".
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In a recording provided to journalists that was allegedly played on the channel, a singer urges listeners to "lock and load your machinegun and move forward" and to show "no mercy".
Haddad denied claims of incitement.
Earlier this month, Israeli forces raided the offices of Al-Hurria radio station, also in Hebron, forcing it to close for six months.
In a separate incident Saturday, police arrested a Palestinian woman, accusing her of planning to carry out an anti-Israeli stabbing attack of the type which have been common over the past month.
Police spokeswoman Luba Samri said border police found a knife on a 27-year-old woman near Hebron's Ibrahimi Mosque, "in what appeared to be an attempt to carry out a stabbing operation against forces there."
Two Palestinians from the Hebron area carried out separate attacks in Tel Aviv and the Etzion settlement bloc Thursday, resulting in five deaths, in one of the deadliest days since an October 1 upsurge of violence.
The army arrested 16 Palestinians in Hebron on Friday night, a military spokeswoman said.
The wave of violence, much of which has been focused in and around Hebron, has left 86 dead on the Palestinian side including an Arab Israeli, as well as 15 Israelis, an American and an Eritrean.
Many of the Palestinians killed have been alleged attackers, while others were shot dead during clashes with Israeli forces.