They declared the gathering an unlawful assembly soon after.
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The rally came just hours after the candidate reached the magic number of pledged delegates needed to secure the GOP nomination.
Police shoved back demonstrators to keep the two groups apart.
Inside the packed Convention Center, Trump gave a rambling speech to cheering supporters, denouncing his critics in the media, naming and shaming reporters at the “failing” New York Times and the Washington Post.
The protesters were waving Mexican and USA flags as they denounced the candidate’s stances on immigration while police cracked down on the demonstrations.
In Fresno, Mr Trump said he had spent 30 minutes before his rally meeting more than 50 farmers who complained to him about their struggles.
Police ordered people to leave the area and warned they would use tear gas. The railing was separating about 1,000 protesters from officers there to monitor Friday’s event.
Pease also referred to the “militarization of the police department” and his plan for what he would do about it if elected.
After the convention centre emptied, clusters of Trump supporters and anti-Trump demonstrators began to mix in the streets, many exchanging shouted epithets and some throwing water bottles at one another.
The visit of presumptive Republican presidential nominee Donald Trump to San Diego sparked angry and almost violent protests that resulted in at least a dozen arrests.
The Democratic presidential hopeful issued a statement saying “In recent days, Donald Trump has said he wants to debate, he doesn’t want to debate, he wants to debate and, now, he doesn’t want to debate”.
Protesters marched around that venue but there was none of the violence that has marked some anti-Trump protests around the country.
Trump, speaking at a rally in San Diego on Friday night, said federal District Judge Gonzalo Curiel, who was appointed to the bench in 2011 by President Barack Obama, should not have allowed the trial to go on.
San Diego is a city on US-Mexico border and is mainly viewed as a binational city because a third of its population is Latino and around 300,000 people cross the border legally every day for work.
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Protesters of presumptive Republican nominee Donald Trump have been showing up to his rallies yelling obscene things and holding up obscene signs for months.
