Numerous migrants may chose to stay in countries along the route, though the Mexican government is already preparing a response.
Mexican authorities, in a bid to soothe Mr Trump's fury and to deter the migrants, without appearing to violate worldwide law, have asked the United Nations to set up a migrant processing centre near its southern border.
Multiple migrants, federal police and journalists were wounded as the crowd hurled rocks and other objects at the security cordon on the Mexican side, an AFP correspondent said.
But at least five U.S. states later refused to send the troops amid an outcry over a since-abandoned White House policy to separate migrant children from their parents at the border.
In a series of tweets, Trump blamed Democrats, leaders of Central American countries and "existing weak laws" for the influx. However, earlier this year Trump made a similar vow over another large migrant caravan, but didn't follow through and it largely petered out in Mexico.
Mexico's ambassador to Guatemala says his country has chose to enforce a policy of "metered entry" since thousands of migrants are clamoring to cross.
Trump, who ran in 2016 promising to tighten USA immigration laws end the inflow of people entering the country illegally, has called for cutting off foreign aid to Guatemala, Honduras and El Salvador if they do not stop the migrants. They also said migrants caught without papers would be deported.
Earlier in the week, the United States president had threatened to cut aid to Honduras and send U.S. troops to the Mexican border. And local media report that growing numbers of migrants have reached the Guatemalan city of Tecun Uman, across the winding Suchiate River from Mexico.
However, although President-elect Andres Manuel Lopez Obrador has said he is confident that agreement with the United States can be reached, the Mexican government has denied that a deal has been done.
"This migration will only continue unless we keep up the pressure and provide the support to make the Northern Triangle of Central America a prosperous and secure place to call home", he wrote in an op-ed in the Washington Post. "Anyone who wants to work in our country will have help, will have a work visa", he pledged. Dozens of Mexican federal police officers are on the border bridge, with hundreds more behind them.
By Thursday, the caravan had dispersed a bit, with the youngest and strongest of the migrants walking ahead together, some boarding buses or trying to hitch rides.
The latest focus is on more than 2,000 Hondurans who left last Saturday from the city of San Pedro Sula.
The new deal, which replaces the North American Free Trade Agreement, has yet to be signed by the three countries.
On Thursday, Trump referred to the caravan as an "assault on our country", citing "criminal elements and drugs pouring in". Trump has since thanked Mexico which has moved to step up security at its border with Guatemala.