The protest was being held outside of the Pomona College graduation, a ceremony which was moved off campus after threats of disruptions.
At one point Sunday afternoon, some skirmishes broke out in the crowd. Officials say some protesters charged at officers and one was arrested after attempting to strike an officer.
Chants of "From the river to the sea" were heard in the crowd, a controversial slogan which some say is just a cry for Palestinian freedom but in other interpretations is seen as an antisemitic call for the destruction of Israel.
Some protesters were also attempting to block entrance to the auditorium, police say.
The LAPD declared an unlawful assembly and started moving the crowd back. Calm seemed to return after the show of force by officers, who were lined up in riot gear on 32nd Street and were blocking off access near the auditorium.
Because the Shrine is near the University of Southern California, access to University Park Campus and USC Village was also closed down.
It was the latest in a string of disruptions to college campuses and graduation ceremonies throughout Southern California and the nation.
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The school announced the change in plans Friday, shifting from a 10 a.m. Sunday ceremony on campus to a 6 p.m. event at the Los Angeles venue.
That was after pro-Palestinian protesters camped out at the graduation stage and threatened to disrupt the ceremonies as part of an effort to pressure the school to divest from Israel amid the ongoing conflict with Hamas.
Parents and students were bused from campus to University Park. Some were not happy about the change, noting that it hurts students who may have supported the protesters' position.
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"Most of the students support those students who are protesting, and they feel like they're punished," said parent Liz Harrell of Glendora. "And the school's not getting punished. We're local but there's a lot of families that aren't and have had to leave. And international students have flights this afternoon that can't (ceremonially) graduate now."
At least 50 protesters showed up outside the Shrine by Sunday afternoon as students were inside getting ready for the proceedings. The crowd seemed to grow larger near the ceremony's start.
Earlier in the day there was a brief security alert at the school's Claremont campus. A driver fled on foot from a UHaul parked near campus, abandoning the vehicle after being questioned by a security officer. Police cleared the area and examined the truck, but found nothing suspicious. The driver later returned, say he only ran because he was nervous.