29 people were arrested, police told CNN. They have since been released. 12 people were injured in the protests.
The incident -- which was caught on video -- came as new Philippines President Rodrigo Duterte visited China to strengthen ties with Beijing.
About 1,000 members of a self-described "newly-formed alliance of national minorities" were protesting the Philippines' "unequal relations with the US, while supporting Duterte's independent foreign policy," the group said in a statement.
Police said the protesters didn't have the proper permit to gather outside the US embassy, according to CNN Philippines. Authorities said they tolerated the demonstrations at first but stepped in when protesters got too close to the building.
Manila Police Chief Superintendent Joel Napoleon Coronel told CNN that two protesters were injured after being hit by the van. He said the driver "was just trying to extricate the police van out of the area because the rowdy protesters were toppling or trying to turn over the van."
However, he stressed that the assessment was the result of an initial report and authorities would still investigate.
Twenty-one protesters were arrested, the National Union of Peoples Lawyers told CNN.
Forging closer ties with China
The Beijing trip is Duterte's first state visit as President.
"I'm going to China to make friends with them and also with Russia," Duterte said recently.
Duterte, who's sought to chart a new foreign policy distancing his country from the United States, enjoys strong support at home with a recent satisfaction poll found that 86% of Filipinos have "trust" in his performance.
Despite his popularity, the majority of Filipinos have a positive view of the United States -- 92% of them held a "very favorable" or "somewhat favorable" opinion of the US in 2015, according to data from the Pew Research Center.
Duterte has made it clear he plans to plot an "independent foreign policy" -- which appears to encompass relying less on US support and warming up to China.
"I would say that China deserves the kind of respect that China now enjoys," Duterte said in an interview with Chinese state-run news agency Xinhua before his visit. "We are ready to cooperate with you, to help us in building our economy and building our country."
Earlier this month he said
he may "break up with America" if it continues to disrespect the Philippines and that President Barack Obama can "go to hell."
China hopes to improve bilateral ties and enhance cooperation in trade, infrastructure and drug control, according to Xinhua.
"This is a historic visit, and presents an opportunity for relations between China and the Philippines to restart on a fresh, more positive footing," said Foreign Minister Wang Yi.
The South China Sea
Though Duterte said
that his country will not hold joint military drills with the US next year, he said their alliance will remain.
"We will maintain our military alliance because ... they say, that we need it for our defense," he said in a speech in Manila.
The reason, many analysts believe, is because of the South China Sea.
An international tribunal ruled in July that China had, among other things, violated the Philippines sovereignty in the South China Sea.
Duterte said he won't bargain on the Philippines territorial rights and will take up the UN ruling with China's leaders -- but won't make any impositions, according to CNN Philippines.
"We continue to insist what is ours, and the tribunal international decision will be taken up. But there will be no hard impositions," he said.
Duterte told Xinhua that he's not interested in going to war over the issue, but that he wants to discuss it with China -- and is willing to pursue joint development of the waters there, under which there are millions of barrels of oil.
"There is no sense in going to war. There is no sense fighting over a body of water," Duterte said. "We want to talk about friendship, we want to talk about cooperation, and most of all, we want to talk about business. War would lead us to nowhere."