House masters, in charge of residential halls at the university, will become known as “faculty deans”.
Harvard Law School is also deciding whether to change its official seal, because of links to slavery.
Student campuses have faced a series of protests over allegations of racism.
Harvard has not accepted that the use of “master” represented a link to slavery, but it has accepted campaigners’ calls for a name change.
It will mean changing the job titles of 24 members of staff – but will not affect other uses of “master”, such as a master’s level degree.
Student campaigners are also calling for a change in the official seal of Harvard Law School, with a sit-in being held this week.
The seal includes the coat of arms of 18th Century college donor Isaac Royall, who as well as establishing the college’s first professorship in law, was a notoriously brutal slaveholder.
A decision on whether to change the seal is expected to be made soon.
Disputes about race and identity have affected many campuses.
Last month, Amherst College, in Massachusetts, accepted student demands to drop links with its informal mascot, Jeffery Amherst, an 18th Century general accused of advocating infecting Native Americans with smallpox.
The protests are part of a wider international campaign challenging historical titles, statues and emblems.
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