USC's peaceful operation allowed students to return for finals and commencement setup, despite canceling the main graduation ceremony.
At Northeastern's commencement, some students waved Palestinian and Israeli flags, but were outnumbered by those displaying other flags.
Approximately 2,500 people have been arrested at around 50 campuses since April 18 due to protests, with 25 arrests at the University of Virginia over the weekend.
On Saturday, police at the Art Institute of Chicago dismantled a pro-Palestinian encampment and arrested 68 people for criminal trespassing.
In Charlottesville, Virginia, students protesting for Palestine were met with riot police on Tuesday.
Protesters were told that tents were against school policy and were asked to leave.
When they refused, police used force to remove them, using chemical irritants and arresting those present.
The university stated that students had been warned to leave and were violating the conduct code.
Virginia Attorney General Jason Miyares defended the police response, stating that outsiders were providing protesters with supplies.
Protests against universities' business dealings with Israel or companies supporting the war in Gaza have been ongoing for weeks, with some demonstrators using intimidation tactics and weapons like bear spray.
At the University of Michigan and other institutions, tensions were high as commencement ceremonies approached, with some schools reaching agreements with protesters to end demonstrations.
A protest took place during a graduation ceremony at Michigan Stadium in Ann Arbor, where around 75 people marched towards the stage wearing traditional Arabic kaffiyehs and chanted "Regents, regents, you can't hide! You are funding genocide!" The protest didn't result in any arrests or significant disruptions, and similar protests occurred at Indiana University, where protesters urged supporters to wear kaffiyehs and walk out during the school president's remarks.
The protests were in response to universities' funding of Israel and the ongoing conflict in Gaza.
Protests against Israel's offensive in Gaza have spread to various college campuses in the US.
The Bloomington campus at Indiana University designated a protest zone outside Memorial Stadium.
At Princeton University, 18 students began a hunger strike to push the university to divest from companies tied to Israel.
Similar hunger strikes were launched at Brown and Yale earlier this year.
The conflict began on October 7 when Hamas militants attacked southern Israel, killing about 1,200 people, mostly civilians, and taking roughly 250 hostages.
In response, Israel launched an offensive in Gaza, which has killed over 34,500 Palestinians, about two-thirds of whom were women and children.
The Israeli strikes have devastated the Gaza Strip and displaced most of its inhabitants.