Palestinian officials told CNN that Jaradat is the 203rd Palestinian to die in Israeli prisons since 1967.
Arafat Jaradat, 30, appeared to have died of a heart attack on Saturday, the Israeli prison service said.
They have spiked notably following last month's death of Arafat Jaradat, a 30-year-old Palestinian, in an Israeli prison.
CNN: Palestinian reported killed by Israeli troops in West Bank
While in custody, Jaradat was checked more than once by a doctor, and no medical problems were found.
The intelligence indicated Jaradat was involved in throwing stones near the Israeli settlement of Kiryat Arba in 2011.
At least 3, 000 Palestinian prisoners are believed to have refused meals on Sunday in protest at Mr Jaradat's death.
Israel's prison service said 3, 000 Palestinian prisoners went on the fast after 30-year-old Arafat Shalish Shahin Jaradat died Saturday.
Jaradat was not on hunger strike and died of an apparent heart attack, Israeli prison services spokeswoman Sivan Weizman said.
Jaradat admitted to the charge, as well to another West Bank rock-throwing incident last year, Shin Bet said in a statement.
The latest descent into violence was precipitated by 29-year-old Hanadi Jaradat, a trainee lawyer from the West Bank town of Jenin.
Palestinians say Mr Jaradat, 30, died from torture, while Israel says a post-mortem was inconclusive and that investigations into his death continue.
The clashes continued on Sunday, fuelled by news of Mr Jaradat's death.
Jaradat, the father of three, worked at a gas station, Rabo said.
Jaradat had been held for interrogation since Monday for a 2011 incident in which an Israeli citizen was injured by rock-throwing Palestinian protestors.
Almost all 4, 500 Palestinian prisoners held in Israeli jails refused food on Sunday in protest at Mr Jaradat's death, an IPS spokeswoman told AFP.
Mr Jaradat's death comes after a week of violent clashes between the Israeli army and Palestinian youths over the continued detention of four hunger strikers.
Arafat Jaradat 30, died inside an Israeli detention facility in February.
Mr Jaradat, a father of two from the village of Sair, near Hebron, in the southern West Bank, died suddenly on Saturday in Israeli's Megido prison.
Hassan Abed Rabo, a spokesman for the Palestinian Ministry of Prisoner Affairs, said it was an "open-ended hunger strike" and "a sign of mourning" for Jaradat.
One man, Arafat Jaradat, died in disputed circumstances in an Israeli jail last weekend - just days after he was arrested following an angry protest in Hebron.
BBC: Two Palestinians held in Israeli jail end hunger strike
Jaradat, from a village near Hebron in the West Bank, was held for interrogation Monday by the Israeli secret service based on intelligence gathered by village residents, Israeli security sources said.
The agency said Jaradat was arrested on Feb. 18 after residents in his West Bank village of Saeer said he was involved in a rock-throwing attack that injured an Israeli citizen.
"In a preliminary response to the killing of our hero the prisoner Arafat Jaradat, we claim responsibility for firing a Grad rocket on Ashkelon at 6:00 (04:00 GMT), " it said in a statement.
Jaradat suffered from back pain and had been injured in the past by a rubber bullet and tear gas canister, the Shin Bet statement said, adding that he was examined a few times by a doctor who detected no health problems, and his interrogation continued.
"The United Nations expects the autopsy to be followed by an independent and transparent investigation into the circumstances of Mr. Jaradat's death, the results of which should be made public as soon as possible, " Robert Serry, the U.N. special coordinator for the Middle East peace process, said in a written statement.
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