Thirteen Palestinians also wounded in the shooting, including a 19-year-old female.
Israeli security forces shot dead a Palestinian in the occupied West Bank refugee camp of Jenin, home of the gunman behind a recent deadly Tel Aviv attack.
Thirteen other Palestinians were wounded by the Israeli shooting on Saturday, according to the ministry, including a 19-year-old female with a bullet to her stomach, the Palestinian health ministry said.
The Palestinian killed was identified as Ahmad al-Saadi who was reportedly a member of al-Quds Brigades (Saraya al-Quds), the military wing of the Islamic Jihad movement.
The Israeli military said its soldiers were conducting a counter-terrorism operation in the area and had opened fire at Palestinian gunmen who shot at them.
Saturday’s raid comes a day after Israel said it shot dead Raad Hazem, 28, the alleged gunman who killed three Israelis and wounded more than a dozen on Thursday in a popular nightlife district of Tel Aviv.
The raid, that lasted for about two hours, began with the army surrounding Hazem’s house and asking his father to turn himself in, which he refused, according to reports.
The Israeli army also raided the village of Burqin near Jenin, reportedly in an operation to arrest former Palestinian prisoner Nour al-Din Hamada. Two injuries were reported in that raid.
Following Saturday’s attack in Tel Aviv, Israeli Prime Minister Naftali Bennett said he had given security agencies “full freedom” to curb a recent surge in violence.
A total of 14 people have been killed in attacks in Israel since March 22, including some carried out by alleged armed men linked to or inspired by ISIL (ISIS).
Over the same period, at least 10 Palestinians have been killed.
The Palestinian movement Hamas, which controls the Gaza Strip, and the Islamic Jihad group praised the Tel Aviv attack – drawing criticism from the UN – but did not claim responsibility.
Thursday’s deadly attack came amid heightened tensions during the Muslim holy month of Ramadan.
During last year’s Ramadan, confrontations between Israeli forces and Palestinian worshippers at the Al-Aqsa mosque compound in occupied East Jerusalem were followed by an 11-day Israeli offensive on Gaza.
Israel killed at least 232 Palestinians in Gaza, including 66 children, and Hamas rockets killed 12 people in Israel, including two children.
Jenin has been a flashpoint throughout the Israeli-Palestinian conflict.
Earlier this month, Israeli security forces killed three Palestinians during an operation to arrest them in the town.
Israel alleged the three men were Islamic Jihad armed group members responsible for an attack in Israel.
The raid, in which four Israeli soldiers were wounded, followed another deadly attack on March 29 in Bnei Brak, an Orthodox Jewish city near Tel Aviv.
In that attack, a Palestinian with an assault rifle killed two Israeli civilians, two Ukrainian nationals and a policeman – a Palestinian with Israeli citizenship.