Bandara, thus, became the second Sri Lankan to win the title after N Thangaraja, who won the trophy last year.
India's Prince Kajotia, who has joined Indian Navy recently, recorded a career best finish after shooting three-over 295 to finish runner-up.
India born Thai golfer, Samarth Dwivedi was third with a score of 300, while coming from behind another Indian Lakhan Singh finished tied fourth along with Amit Kumar at 303.
After taking a lot of pressure on himself, the 24-year-old Bandara dropped two shots and made a double bogey on 10th.
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Number one on Sri Lanka amateur circuit, Bandara got confused in choosing the clubs on 11th hole and he used 3-wood for the tee shot where in he normally uses his 52 wedge. His best shot of the tournament came on the finishing hole where he rescued the ball from a difficult condition as he landed his tee shot in right bushes but managed a par with advice from his caddy.
Another highlight of the day was a hole-in-one on seventh hole by Devendra Singh, who finished 22nd. Lakhan Singh took the longest drive challenge prize on sixth hole, which was also a hat-rick in NCR Cup by him. Sunny Nagar won the straightest drive on 10th hole.