Calicut University beat Sant Baba Bhag Singh University 2-0 in the final.
Kerala University went down 1-2 to Sant Baba Bhag Singh University, Jalandhar, while Punjabi University edged out Adamas University, Kolkata, 1-0 to complete the semifinal line-up.
MG University's M D Roshan and Kerala University's Jebin scored hat-tricks.
Panjab University thrashed Sant Gadge Baba Amravati University 7-0, while Guru Nanak Dev University thumped Rajasthan University 6-2.
West Bengal's Adamas posted the biggest win (7-0) on the opening day of the inter-zonal tournament.
MG played out a goalless draw with Kerala University in their final semifinal league game to clinch the title.
The four teams that qualified for the inter-zonal competition are competing in a round-robin event to decide final standings.
In another match, Karpagam Academy drubbed Yenepoya University 3-0.
Annamalai University thrashed St Peter's Institute of Higher Education & Research 10-0 in another match.
Nimshad Roshan and Arjun V scored a brace each for the winners.