Mrs Clinton spoke over the shouting, saying if elected she would carry on the work on President Barack Obama.
The group of 10 Black Lives Matter protesters were quickly escorted away.
They have interrupted campaign events to highlight police brutality, racism and mass incarceration.
The activists have mostly targeted Democrats – including Mrs Clinton and her chief rival Vermont Senator Bernie Sanders.
Mrs Clinton and Mr Sanders have responded to the protests with policy proposals, meeting activists and talking about racial issues on the campaign trail.
The Black Lives Matter movement was originally formed after George Zimmerman, a Hispanic man in Florida, was acquitted of the shooting death of black teenager Trayvon Martin.
It grew to greater prominence after a white policeman killed Michael Brown – an unarmed black teenager – in Ferguson, Missouri, last year.
The protest movement has continued to gain strength over the past year after several controversial police-involved deaths of black people including those of Freddie Gray and Sandra Bland.
‘Let her talk’
Friday’s rally was entitled “African Americans for Hillary”. Guests included pop singer Usher and civil rights activist and Congressman John Lewis.
The crowd of about 2,000 chanted “Let her talk!” and Mr Lewis asked them to stop.
“I’m sorry they didn’t listen, because some of what they demanded I am offering and intend to fight for as president,” Mrs Clinton said. “We have to come together as a nation.”
In 1994 Mrs Clinton lobbied for one of the largest crime bills in US history, the Violent Crime Control and Law Enforcement Act, which provided billions for prisons. The law also introduced the “three strikes” policy, which called for mandatory life imprisonment without parole for federal offenders with three or more felony or drug trafficking convictions.
Mrs Clinton has changed her position since she has been on the campaign trail, calling for the end of mass incarceration and expressing her concern over police violence and black people.
On Friday, she also proposed a legal ban on racial profiling by police.
The policy would forbid federal, state and local officers from “relying on a person’s race when conducting routine or spontaneous investigatory activities,” unless they have information linking a suspect to a crime.
And she said she supported the “ban the box” movement, an effort to prevent job applicants from being disqualified because of their criminal history.