About 7,000 people were in attendance across two separate rallies, according to the Australian Broadcasting Corporation.
"While the organizers had confirmed separate locations and routes for their events, protesters from one group moved to … counter-protest," police said in a statement, Anadolu reported.
The detainees were later released and will receive a summons to appear in court.
During the rallies, one person was seen burning an Israeli flag.
Liberal Senator and Shadow Home Minister James Patterson was among several political figures attending the pro-Israeli demonstration.
Sunday's events came after a week of protest activity throughout Melbourne, the capital of southeastern Victoria state.
Pro-Palestinian encampments have been established at a number of university campuses across Australia.
In Melbourne, students were this week occupying a building in the city's central business district belonging to the University of Melbourne.
On Saturday, pro-Palestinian demonstrators stormed the venue of a Labor Party conference.
SD/PR