Commotion prevailed at the University auditorium when the students shouted slogans against the former Rajya Sabha MP who had arrived to deliver a talk on Tamil culture.
However, the students were whisked away from the venue by the police.
Around 20 students were taken into custody and released later, Superintendent of Police S Venkatasamy said.
Sources said the BJP leader was there to participate for an event on birth anniversary celebrations of Dr B R Ambedkar.
Earlier in the day, Vijay had visited the Puducherry government-run Bharathiyar Palkalaikoodam, a multi-cultural institution offering courses in fine arts.
Later, he told reporters that steps would be taken to digitise the documents and letters of nationalist poet Subramania Bharati.
The BJP leader had on April 7 kicked up a row after he appeared to suggest during a panel discussion on a news channel that Indians cannot be called racist as they live with those from south India who are "black".
The BJP leader's controversial comments had sparked an outrage.