The Ivy League university's move to end the role of law professor Ronald Sullivan Jr and law school lecturer Stephanie Robinson, Sullivan's wife, at Winthrop House follows protests over his representation of Weinstein.
Sullivan and Robinson in 2009 became the first African-American faculty deans in Harvard history when they took their positions at Winthrop House, one of several undergraduate residences at the Cambridge, Massachusetts, university.
Their terms as faculty deans were scheduled to end on June 30. Harvard College Dean Rakesh Khurana said in a statement that he had decided not to keep them in their roles at Winthrop House beyond that date.
"Over the last few weeks, students and staff have continued to communicate concerns about the climate in Winthrop House to the college," Khurana said.
"The concerns expressed have been serious and numerous. The actions that have been taken to improve the climate have been ineffective, and the noticeable lack of faculty dean presence during critical moments has further deteriorated the climate in the house," Khurana said.
Khurana has previously said Sullivan's decision to join Weinstein's legal team was a matter of academic freedom and that everyone is entitled to a vigorous legal defense.
Sullivan and Robinson continue to hold their positions at Harvard Law School.
Sullivan and Robinson said in a joint statement that they were "surprised and dismayed" by the decision.
"We believed the discussions we were having with high level university representatives were progressing in a positive manner, but Harvard unilaterally ended those talks," they said.
In January, a judge approved Weinstein's request to have Sullivan join his legal team.
Prosecutors in New York accuse Weinstein, 67, of forcibly performing oral sex on a woman in 2006 and raping another woman in 2013. Weinstein faces five criminal charges, including rape, and could be sentenced to life in prison if convicted.
He has pleaded not guilty to the charges.
More than 70 women have accused Weinstein of sexual misconduct. He has denied all accusations and said any contact was consensual.Students at Winthrop House staged a sit-in this month to protest Sullivan's defense of Weinstein, according to a report at the time in the Harvard Crimson student newspaper. Students denounced Sullivan in other actions earlier this year.