Customs and Border Protection said the non-lethal measures were not aimed at those who were actively climbing the fence, but at people who were throwing rocks south of the borderline.
"These countermeasures successfully suppressed the rock throwers causing them to flee the area," CBP said in a statement.
A Homeland Security spokesperson described the group as “a violent mob.”
Multiple children were among the migrants attempting to cross, and officers reported seeing some of them lift “toddler-sized children up and over the concertina wire.”
Border Patrol also used smoke devices and pepper spray on the migrants. Twenty-five people were arrested, including two teenagers who attempted to cross, according to CBP. They were not injured.
"Agents observed several individuals throwing rocks who appeared to have prepared themselves for the assault by applying lotion to their faces to counter the effects of chemical munitions," Rodney Scott, chief patrol agent of the U.S. Border Patrol's San Diego sector, said in a statement posted on Instagram. "Several arrests were made, all individuals from central America. No injuries were sustained by either the agents or individuals arrested."
The incident is undergoing an internal review, a standard practice when agents use nonlethal deterrents, according to CBP guidelines.
Border Patrol came under scrutiny in December for using tear gas when a large group of migrants previously attempted to cross into San Diego.
Although CBP policy says agents are not allowed to use tear gas on pregnant women and children, several women and children were among the group targeted by the gas used at the time.
Border Patrol arrested 42 migrants after the November incident, but criminal charges were not filed.
The migrants arrested during Monday night’s incident will likely face deportation proceedings, but will also have the opportunity to apply for asylum.