The Republican Presidential candidate was speaking at Radford University in Virginia on Monday when the group started chanting: “No more hate! No more hate! Let's be equal, let's be great!"
“Get them out of here please, get them out…get them out,” Mr Trump ordered, before asking: “Are you from Mexico?”
Footage showed the students leaving the packed auditorium in a long column while chanting and waving Black Lives Matters posters.
A Time magazine photographer attempting to get a photo as they passed was caught on camera being thrown to the ground by a Secret Service agent, causing some demonstrators to break off in concern.
Mr Trump paused his speech as the disruption continued, saying: “Get them out of here please…trouble, nothing but trouble.”
As the rally settled back down, he told supporters: “Folks, you’re going to hear it once – all lives matter.
“You have some people who are just looking for trouble and if you’re looking for trouble, I don’t want to talk. We have to act tough, and we have to act swiftly.”
Just hours later, at another rally at Valdosta State University in Georgia, another group of Black Lives Matter protesters were removed after being spotted standing on bleachers in a silent protest before Mr Trump's speech began.
They claimed Secret Service agents told them Mr Trump had demanded they be removed before he started speaking but a spokesperson for his campaign later said it was not the candidate’s request.
“I think we got kicked out because we’re a group of black people and I guess with what’s going on in America, they’re afraid we’re doing to say something or do something, but we just really wanted to watch the rally,” one of the protesters told USA Today while being escorted away.
Another young woman said the group wanted to “make a statement with our attire”, evoking the Black Panthers.
“We weren’t starting any trouble, we weren’t saying anything, we came in together as a group to see what the Presidential candidate had to offer to our campus, to our community and our country,” she added.
The sight of the visibly upset students being led outside by police caused discomfort university that was a whites-only campus until 1963, USA Today noted.
The rallies came a day before one of the most important days in the US Presidential race, Super Tuesday, when when 11 states hold contests for the Republican and Democrat selections.
Additional reporting by AP
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