Despite a 1-over par 71, the Kolkata lad was 7-under 203 for the tournament.
With the fight virtually being reduced for minor placing, Manu Gandas was placed second at 214 while Tapendra Ghai was third, just a stroke behind Manu.
Shubham Narain was in the fourth position at 217.
Yuvraj Sandhu, Pukhraj Singh Gill and Prakhar Asawa were tied for the fifth position at 219.
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But soon he was in trouble incurring a bogey on the par-4 third.
However, the 15-year-old played some steady golf and made back to back birdies on the seventh and eighth before making a double on the ninth.
An aggressive approach on his back nine saw him gain mixed results with a bogey on the 11th and a birdie on the 14th which was followed by a double bogey on the 15th.
Successive birdies on the next two holes ensured that he returned home with just a shot over the par.
"Actually I thought of taking it hole by hole and then if need be try and attack. I admit that the strategy was not too successful as I lost some shots which could have been avoided," added the leader.
Top scores after 54 holes (Cat A & B) 203 Viraj Madappa (62, 70, 71); 214 Manu Gandas (68, 72, 74); 215 Tapendra Ghai (75, 68, 72); 217 Shubham Narain (68, 73, 76); 219 Yuvraj Sandhu (72, 73, 74), Prakhar Asawa (73, 71, 75), Pukhraj Singh Gill (68, 75, 76); 221 Mohan Sardar (73, 73, 75), Kartik Sharma (Cat B) (74, 73, 74); 222 Feroz Singh Garewal (76, 73, 73), Arjun Prasad (Cat B) (69, 80, 73).