The winner will now travel to Indonesia to compete at the Manchester United Regional Final 2012 on May 27.
Chandigarh's Samuel Lalmuanpuia scored twice during the extra time to help his team clinch the coveted prize.
Both teams were evenly poised till the second leg of the game here. Eventually, the game was decided when the Mizoram-born Lalmuanpuia scored during the fourth minute of extra time from a freekick and found the net again two minutes later.
Nike Manchester United Premier Cup (MUPC) is a tournament that is held at grassroots level to promote the sport.
"Over the years, Nike MUPC is serving as a platform to identify young talent. This is at the core of our brand to promote the sport," Nike Marketing Director Avinash Pant told reporters here.
Veteran Baichung Bhutia, who was present at the event, said the tournament will continue to be a platform for young footballers to showcase their talent.