The San Ysidro border post -- the busiest crossing on the US-Mexico border -- was closed to north and south traffic and pedestrians for several hours following the incident, the US Customs and Border Protection (CBP) office in San Diego, California said.
The migrants, mostly from Honduras, are part of a "caravan" loudly condemned by President Donald Trump.
The shutdown took place only three days after Trump threatened to close the "whole border" with Mexico if "it gets to a level where we're going to lose control or people are going to start getting hurt."
Mexican Interior Minister Alfonso Navarrete accused some of the migrants of attempting to cross from Tijuana in a "violent way," and said they would be deported.
"Far from helping the caravan, they are hurting it," he told the Milenio television network.
Video clips posted on Twitter showed crowds of migrants dashing across a shallow concrete riverbed toward the United States.
The sudden rush overwhelmed Mexican police, who were deployed with large clear shields and full riot gear.
Some 5,000 migrants have been gathering in Tijuana in hopes of entering the US.
Secretary of the US Department of Homeland Security (DHS) Kirstjen Nielsen accused the migrants of seeking to harm US border patrol personnel "by throwing projectiles at them."
"As I have continually stated, DHS will not tolerate this type of lawlessness and will not hesitate to shut down ports of entry for security and public safety reasons," she said in a statement, adding that US officials would "seek to prosecute" offenders.
'Are we in the US yet?'
At least 500 migrants, including women and children, had been taking part in a peaceful demonstration in Tijuana before dashing toward the border in an attempt to clamber over a first metal fence.
"Are we in the United States yet?" some asked in desperate tones.
Several hundred made it over the first barrier and were trying to cross a second -- topped with spikes -- when US border agents began firing tear gas and rubber bullets at them. US helicopters flew low overhead, according to an AFP journalist on the scene.
The migrants covered their faces to protect themselves from the acrid gas. Mothers clutched their young children close as they fled for safety.
There were cries of pain, desperation and frustration as the crowd swirled over the border line and back.
Some migrants shouted that they only wanted to make their way to a better life.
"They told us that if we crossed (the first barrier) they would give us asylum, because we were already in the United States," said Flor Jimenez, a 32-year-old Honduran woman.
"But now it seems that they want to kill us, and we got very scared," said Jimenez, who managed to reach the second border fence with her husband, her sister and her young daughter.
Amid the clouds of stinging gas, the crowd of migrants, including Jimenez and her relatives, returned to Tijuana.
A reported asylum deal
Trump has deployed some 9,000 troops along the border to support Customs and Border Protection agents.
Approximately 5,000 migrants reached Tijuana over the past week, after an exhausting trip of up to 2,500 miles (4,000 kilometers) covered in just over a month. Many were fleeing violence and poverty in Honduras hoping to find asylum in the US.
To enter the US legally, migrants must apply for asylum, but the wait for those requests to be processed can last up to a year.
Trump signed a proclamation earlier this month stating that asylum claims could only be filed at US ports of entry, but a federal judge in San Francisco temporarily blocked the order, pointing to "irreconcilable conflicts" with immigration law.
The Washington Post reported Saturday that the Trump administration had gained support from the incoming administration of Andres Manuel Lopez Obrador -- who takes office on December 1 -- for a plan to require asylum seekers to wait in Mexico for their applications to be processed.
But after the Post report was met by stiff criticism in Mexico, incoming administration officials said that the agreement was not yet final.
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