US Border Patrol shot tear gas and rubber bullets at a group of migrants, including toddlers, as members of the caravan tried to storm the border.
Children were screaming and coughing in the mayhem at the San Ysidro Port of Entry when American agents tried to push the surging Central Americans back.
They started to use crowd control on Sunday afternoon when migrants tried to cut a hole in the concertina wire gap on the Mexican side of the fence.
The tensions prompted US officials to close the crossing between Tijuana and San Diego, stopping thousands of people travelling legitimately between the US and Mexico.
Homeland Security Secretary Kirstjen Nielsen said she would not put up with this 'lawlessness' and threatened harsh punishments on anyone who 'anyone who destroys federal property, endangers our frontline operators, or violates our sovereignty'.
Mexico also vowed to deport about 500 migrants who tried to 'violently' and 'illegally' cross the U.S. border on Sunday, according to the Mexican Interior Ministry in a statement.
The statement added that Mexican authorities had contained the protest at the crossing between Tijuana and San Diego.
Despite heightened tensions there, Mexico said they would not send military forces to control 7,417 migrants from a caravan currently amassed at the U.S.-Mexico border.
Honduran migrant Ana Zuniga, 23, said she saw migrants open a small hole in concertina wire at a gap on the Mexican side of a levee, at which point U.S. agents fired tear gas at them.
'We ran, but when you run the gas asphyxiates you more,' she told the AP while cradling her 3-year-old daughter Valery in her arms.
Mexico's Milenio TV also showed images of several migrants at the border trying to jump over the fence.
Yards away on the U.S. side, shoppers streamed in and out of an outlet mall.
U.S. Border Patrol helicopters flew overhead, while U.S. agents held vigil on foot beyond the wire fence in California.
'Today, several migrants threw projectiles at the agents in San Diego,' Customs and Border Protection tweeted on Sunday.
'Border Patrol agents deployed tear gas to dispel the group because of the risk to agents' safety.
'Several agents were hit by the projectiles. The situation is evolving and a statement is forthcoming.'
The Border Patrol office in San Diego said via Twitter that pedestrian crossings have been suspended at the San Ysidro port of entry at both the East and West facilities.
All northbound and southbound traffic was halted.
Earlier Sunday, several hundred Central American migrants pushed past a blockade of Mexican police who were standing guard near the international border crossing.
They appeared to easily pass through without using violence, and some of the migrants called on each other to remain peaceful.
They convened the demonstration to try to pressure the U.S. to hear their asylum claims and carried hand-painted American and Honduran flags while chanting: 'We are not criminals! We are international workers!'
A second line of Mexican police carrying plastic riot shields stood guard outside a Mexican customs and immigration plaza.
That line of police had installed tall steel panels behind them outside the Chaparral crossing on the Mexican side of the border.
Migrants were asked by police to turn back toward Mexico.
More than 5,000 migrants have been camped in and around a sports complex in Tijuana after making their way through Mexico in recent weeks via caravan.
Many hope to apply for asylum in the U.S., but agents at the San Ysidro entry point are processing fewer than 100 asylum petitions a day.
Irineo Mujica, who has accompanied the migrants for weeks as part of the aid group Pueblo Sin Fronteras, said the aim of Sunday's march toward the U.S. border was to make the migrants' plight more visible to the governments of Mexico and the U.S.
Tijuana Mayor Juan Manuel Gastelum on Friday declared a humanitarian crisis in his border city of 1.6 million, which he says is struggling to accommodate the crush of migrants.
Mexico's Interior Ministry said Sunday the country has sent 11,000 Central Americans back to their countries of origin since Oct. 19. It said that 1,906 of them were members of the recent caravans.
Mexico is on track to send a total of around 100,000 Central Americans back home by the end of this year.
Homeland Security Secretary Kirstjen Nielsen tweeted on Sunday: ‘This AM, @CBP was forced to close the #SanYsidro POE to ensure public safety in response to a large # of migrants seeking to illegally enter the US.
‘@DHS will not tolerate this type of lawlessness & will not hesitate to shut down POEs for security reasons.
‘We'll seek to prosecute to the fullest extent of the law anyone who destroys federal property, endangers our frontline operators, or violates our sovereignty.
‘#CBP along w other DHS, federal, state & local law enforcement, & the @DeptofDefense, have a robust presence along the SW Border and at our POEs. We remain in close contact with Mexican authorities and are committed to resolving this situation safely in concert with them.’