The Dalit professor is a senior faculty member in the Sanskrit Vidya Dharam Vigyan (SVDV) department where Khan has been appointed.
"I was sitting in a classroom when some students barged in and started abusing me in foul language. They asked me to stop supporting a Muslim's appointment to the faculty.
"I felt unsafe and came out. Some of the students then hurled stones at me and later caught up with me and shoved and pushed me. I could escape because a stranger gave me a lift on his scooter," Professor Shanti Lal Salvi told reporters here, following the Monday's incident.
Salvi alleged a colleague had instigated the students but would not name him before the media.
"I have complained to Vice-Chancellor Rakesh Bhatnagar against a professor of the department and some students," he said.
A student, who was a part of the group that had accosted Salvi, said they had only asked the professor to stop supporting Khan and never attacked him.
Some students of the Sanskrit Vidya Dharma Sankay department have been protesting Khan's appointment on the ground that a Muslim cannot teach Hindu religious texts, which the department's syllabus includes.
There has been speculation that Khan may be shifted to the department of Samhita and Sanskrit, part of the university's faculty of Ayurveda, or the Sanskrit department of the arts faculty as a compromise.
He has appeared in interviews held by the two departments, on November 29 and on December 4.
Meanwhile, no classes have been held in the Sanskrit Vidya Dharma Vigyan department since November 8, the day after Khan's appointment.
Chief proctor O.P. Rai met the student protesters on Monday and said Khan's appointment would soon be discussed at the executive council of the university.
The semester examinations have also been postponed due to protests. "The next date of the semester examination in the department will be announced soon," the proctor told reporters.
( With inputs from IANS )