Over 300 ultra-Orthodox men, mostly from the Breslov Hassidic sect, arrived at the site in Halhul city, located 5 kilometers (3.1 miles) north of al-Khalil on board a number of buses early on Sunday, and broke into the tomb amid protection by Israeli troopers, Arabic-language Safa news agency reported.
Israeli forces had deployed several military vehicles on the streets leading to Jonah's Tomb, and snipers were positioned on rooftops overlooking the area.
Clashes erupted when young Palestinian men started hurling stones and empty bottles Israeli troopers and settlers.
Israeli soldiers, in return, fired rubber-coated steel bullets, stun grenades and tear gas canisters to disperse the crowd. No injuries were reported.
Meanwhile, more than a hundred Israeli extremist settlers and religious students have stormed the al-Aqsa Mosque compound in the Israeli-occupied Old City of East Jerusalem al-Quds.
On Sunday morning, a total of 102 people forced their way into the holy site through the Bab al-Magharibah under tight protection of several groups of Israeli soldiers and special police forces.
The settlers performed acts deemed provocative by Palestinians. Some of them toured the mosque courtyard, while the rest converged near the Golden Gate, also known as the Gate of Mercy, on the eastern flank of the mosque and read Talmud verses out loud.
The occupied Palestinian territories have witnessed new tensions ever since Israeli forces introduced restrictions on the entry of Palestinian worshipers into the al-Aqsa Mosque compound in East Jerusalem al-Quds in August 2015.
Some 300 Palestinians have lost their lives at the hands of Israeli forces in the tensions since the beginning of October 2015.
The Tel Aviv regime has tried to change the demographic makeup of Jerusalem al-Quds over the past decades by constructing illegal settlements, destroying historical sites and expelling the local Palestinian population. Palestinians say the Israeli measures are aimed at paving the way for the Judaization of the city.
The al-Aqsa Mosque compound is a flashpoint Islamic site, which is also holy to the Jews. The mosque is Islam’s third holiest site after Mecca and Medina in Saudi Arabia.