Among the protesters were students from Balad and other Arab political parties.
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Watch Arab students hold moment of silence
Haifa University Student Union Chairman Yossi Shalom said, "It is shocking and painful to see the protesters standing in defiance on Israeli soil while the country mourns the death of three civilians.
"The situation in the south is intolerable, and this morning we launched a volunteer system of students interested in hosting families from the south. The response is amazing and we're rediscovering the beauty of Israeli society."
Moment of Silence at Haifa University (Photo: Ronit Moskowitz)
Haifa Mayor Yona Yahav sent a letter to Haifa University President Amos Shapira, in which he wrote: "We are shocked and disgusted by the ceremony in which Israeli students stood for several minutes in memory of the murderer, in an act of intentional provocation."
He called on the university to strongly condemn the event and make certain that it does not repeat itself.
'Israeli government responsible for killing'
Students from Haifa University demonstrated in the city against the operation on Wednesday as well.
One of the students told Ynet, "We'll continue our struggle against the offensive in the Gaza Strip. The Israeli government is responsible for killing people. Netanyahu wants to start a war at any cost so that he can win the elections at the expense of Gazan casualties."
Another student called on the Israeli government to stop the offensive in the Gaza Strip. "We don't want war. The government has proved to be a destructive government which has one main goal – to assassinate people in Gaza without considering the families' social and economic situation."
She promised that it won't be the last protest. "We'll take additional steps so that the entire country hears what we have to say about what is happening in Gaza."
The Arab students were faced by a counter-protest of Jewish students. One of them, a Nahariya resident, said: "Unfortunately, the Arab students are demonstrating against Jabari's assassination today. Such a protest means that the Arab students support terror against the State of Israel."
Meanwhile, in Tel Aviv University and the Hebrew University in Jerusalem, dozens of students attended a protest rally against the Israeli offensive in Gaza.
Haifa University said in response that "the university supports IDF soldiers who are defending the State of Israel and sends its condolences to the families of the people killed in Kiryat Malachi. The university's management takes and will take every legal measures at its disposal to prevent any provocation on its territory.
"As for today's event – it was a gathering held without the university's consent. A small number of Arab students gathered, faced by Jewish students, and the whole thing ended within a few minutes."
The Arab Higher Monitoring Committee said in a statement, "We oppose the attack on Gaza and the assassination of Palestinian people and leaders. Palestinian blood is more precious than the bloodshed the fascists are taking advantage of for publicity ahead of the Knesset elections.
"If the Israeli government thinks that this is the way to provide the settlers in the south with security, they are wrong. The Israeli government must take full responsibility for the people being killed on both sides – the Palestinian and the Israeli. The ongoing occupation of Palestinian lands is the main reason for everything that is happening here today."
Hassan Shaalan, Shahar Chai and Ahiya Raved contributed to this report