Vijay alias Tamil Selvan (18) and Karthik Kumar (20) were booked under the Tamil Nadu Prevention of Harassment of Women Act in connection with the November 23 incident, a police release said.
Selvan, engaged in selling mineral water cans, and Kumar, an engineering student, were arrested and produced before a court which remanded them to judicial custody.
The video went viral on the social media, following which a case was lodged by the police.
Chennaiyin FC, which won the match 3-0, had condemned the "unbecoming behaviour" of a section of its fans against a group of NEUFC fans.
NEUFC owner, Bollywood actor John Abraham, too had slammed the incident and said the team stood by the fan who was "victimised".