Tripathi, who was scheduled to retire on November 30, has gone on "indefinite leave", BHU officials said.
The development comes amid indications from top HRD ministry sources that the central government was upset with the manner in which he handled the entire episode, including a protest by women students following an incident of alleged harassment.
University administration called the police to the campus.
A number of students were injured in the police lathi-charge.
However, Tripathi had claimed he would resign if asked to go on leave.