The Republican Presidential candidate stopped his speech in Louisville several times as several groups of demonstrators were removed.
“Get out of here,” he said, before repeatedly shouting “out, out, out” as a black woman was pulled through the crowd.
She was shoved by several Trump supporters and could be seen saying “stop pushing me”, as she was jostled by a group of men shouting and gesturing aggressively in her face.
Shaun King, a New York Daily News journalist, reported that some of the men seen in the footage were neo-Nazis and members of the far-right Traditionalist Worker Party.
"Police looked on as she was shoved," he wrote on Twitter.
The struggle was captured by WLKY News, which contacted the young woman on Tuesday evening. She told reporters she was well but “just trying to process everything”.
Similar scenes were repeated several times during the course of the rally at the Kentucky International Convention Center, where former New Jersey Governor Chris Christie had introduced Mr Trump as “the next President of the United States”.
“Oh look what we have here, some wonderful people, aww,” Mr Trump said as another group of white student protesters were removed. “Get out of here, get out, get out.”
“Don’t hurt him,” he added as another young man was pushed through the packed auditorium by a secret service agent, being pushed and shouted at by members of the crowd.
“See, if I say go get him, I get in trouble with the press – the most dishonest human beings in the world.”
The Kentucky Kernel, the University of Kentucky student newspaper, said Black Lives Matter protesters, as well as supporters of Mrs Clinton and her fellow Democratic candidate Bernie Sanders were among those ejected from the event.
The footage provoked a new wave of outrage following another day of controversy on Monday, when black demonstrators were thrown out of two Trump rallies at universities in Virginia and Georgia.
They chanted “No more hate! No more hate! Let's be equal, let's be great!" before being led out.
The demonstrations come as a furore continues to rage over his failure to condemn the Ku Klux Klan on CNN.
But the successive waves of controversy did not stop Mr Trump taking an important lead on Super Tuesday, the most important day in months of US primaries to select Republican and Democrat Presidential candidates.
Both he and Hillary Clinton won at least seven of the 11 states voting, putting them far ahead of their nearest rivals.
The result increased the likelihood of a Trump-Clinton showdown in the November election, offering voters what would likely be the starkest contrast in presidential candidates seen for many years.
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