Bagan scored through Jeje Lalpakhlua (13th minute) and Glen Cornell (30th, 45+2), while Salgaocar FC pulled one back in the 71st minute through Darryl Duffy.
Salgaocar were reduced to 10 man in the second half after Gilbert Oliveira, who had altercation with substiute Bikramjit Singh, lost his cool and exchanged blow on him prompting referee Rowan Arumughan to give him marching orders.
Bagan, who are leading the table at the end of the first leg, played as a unit with Sony Norde, Jeje and Kastumi Yusa cordinating the midfield well and proving a threat to the rival defense.
Bagan, who missed Luciano Sobrosa and Pronoy Halder due to suspension, did not feel their absence as the defence put up a solid performance and kept Darryl Duffy quiet even as Salgaoacar failed to trouble the rival defence.
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Lenny Rodrigues, who played his first match, executed the move from the left and played the ball to Sony Norde who in turn gave back the ball to Leny whose attempt at the goal was blocked by keeper Karanjit Singh. The rebound fell at the foot of Jeje Lalpekhlua who found the back of the net even as defender Eder dived but could not put the ball out of danger.
Salgaocar who made lot of mistakes in the midfield conceded another goal in the stoppage time of the first half.
Cornell Glen who got the ball on top of the box sprinted down and beat keeper Karanjit Singh with a low shot at the far corner of the net to take Bagan to a 3-0 lead at half time.
Changing over, Bagan continued to impressed in the midfield but could not score more goals as they kept the ball among themselves for better part.