Daniel Bedemi's foul on Edu earned Sporting a penalty, but the Brazilian's set piece was saved by Gumphe Rime.
In the other match, the airmen drew first blood in the tenth minute.
A Tapan Maity centre from the left was headed by Opara, and Pune FC goalkeeper M. Balaji managed only a partial clearance. Bopara was quick to let go a left footer into the net.
Down 0-1 at the breather, Pune FC drew parity in the 48th minute when Japanese Arata stabbed home a Je Je Lalpekhnua final pass.
But the deadlock lasted for only eight minutes. Pune defender Caitani Costa committed a handball inside his own box and referee Mrinangshu Bhattacharya had no hesitation in signalling a penalty. Ravinder Singh scored the winner.