According to San Diego Police, 35 people were arrested. There was no property damage and no injuries reported, police added.
The roughly 1,000 demonstrators were gathered on both sides of the street outside the San Diego Convention Center.
Some protesters holding Mexican flags and flags from other countries yelled, "Dump Donald Trump."
Trump supporters chanted, "You can't vote," and, "Build that wall!"
A helicopter loudspeaker and ground loudspeakers repeatedly made announcements that unlawful assembly was declared, and anyone in the area would be arrested if they stayed.
Trump took to Twitter to thank the San Diego Police Department, while referring to the anti-Trump protesters as "thugs." He wrote, "Fantastic job on handling the thugs who tried to disrupt our very peaceful and well attended rally. Greatly appreciated!"
ABC News' Alex Stone contributed to this report.