The demonstrators set fire on pictures of Netanyahu, saying that his visit to the city only aimed at fulfilling his political ambitions.
“We, as Palestinian citizens, are angry of Netanyahu storming the city of Hebron,” said a demonstrator.
“We feel provoked to be used as Palestinian citizens, for our city to be used, for our mosque to be used, for our properties to be used as part of this political election campaign by Netanyahu, so he would gain the votes of the extremist Israeli right,” the protester added.
Palestinian officials have also condemned the visit, describing it as provocative.
The Palestinian president’s spokesman says Netanyahu’s move may spark a religious war, warning about consequences of the “grave escalation”.
Palestine’s resistance movement, Hamas, also slammed the provocative move, saying Israel’s attempt to change the history of al-Khalil will be futile.
During the trip, which was made under tight security, Netanyahu made a speech in the Ibrahimi mosque, which is sacred to both Muslims and Jews.
In an apparent effort to rally right-wing votes for an election two weeks away, the Israeli premier said in his speech that Jewish people will never leave the area.
“Hebron will not be cleansed of Jews. We are not strangers in Hebron. We will remain in it forever,” he claimed.
The speech was delivered right at the place where an armed Israeli settler had killed 29 Palestinians in 1994.
Around 1,000 heavily guarded illegal settlers live among 200,000 Palestinians in al-Khalil.
In the April elections held in the occupied territories, just 7.5 percent of al-Khalil Jewish settlers voted Netanyahu’s Likud Party, with most backing more rightist parties, census data show.