Meanwhile, Kargil martyr's daughter Gurmehar Kaur, who started a facebook campaign against ABVP, left Delhi following rape threats.
The students held posters with messages like "Your nationalism is not above our democracy".
The protesters, mainly comprising students of left forums like AISA, shouted slogans "ABVP Go Back" and "Azaadi" as the march made its way through the roads of North Campus towards the Arts Faculty building.
The gates of the colleges falling on the route of the march, which began from the gates of Khalsa College, were shut.
"We are marching to reclaim the space to debate and discuss. It is about the freedom to coexist, yet disagree," a student said.
There was heavy police deployment to prevent a rerun of the clashes that were witnessed between ABVP and AISA last week following cancellation of an event at Ramjas College after activists of the RSS-backed students' wing objected to the invitation to JNU student leaders Umar Khalid and Shehla Rashid.
One of the faculty members, marching with the students, alleged that the university has been "taken over" and that authorities were not acting to prevent it.
Police registered a case of sexual harassment and criminal intimidation against unknown persons in connection with the "rape threats" allegedly received by Gurmehar Kaur.
The case was registered following a complaint received from Delhi Commission for Women on behalf of Delhi University student Gurmehar Kaur (20).
The FIR was registered under sections 354A (Sexual harassment and punishment for sexual harassment), 506 (Punishment for criminal intimidation) of IPC and section 67 of the IT Act against unknown persons, said Dependra Pathak, Special Commissioner of Police (Southwest) and Delhi Police spokesperson.
Earlier, LSR student Gurmehar Kaur withdrew from her social media campaign against the ABVP after allegedly receiving threats from the members of the RSS-backed outfit and being trolled by the ruling BJP leaders and ministers.
Yesterday, the ABVP had taken out a 'Tiranga march', "to save the nation", from Ramjas College to the Arts Faculty.