Pratap will now meet the top seed Karan Taunk of Jamshedpur who quelled the challenge of Md. Sajib Ali from Bangladesh on the 18th hole.
Twenty-two-year-old Pratap, who is related to the more famed golfing family of Arjun Atwal, had earlier beaten third seed Udayan Mane in the pre-quarterfinal and shown 11th seed Samarth Dwivedi the door in the next round.
Up against the experienced Gagan, Pratap did not show any signs of nervousness as the battle began with both the players making birdies.
However, he lost a hole when made a bogey on the sixth. Winning two more in the last three holes put Pratap in a comfortable 4-up position at the turn.
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The status remained the same until the 15th hole where Gagan made a bogey against Pratap's par to hand his younger opponent a well-deserved victory.
"After the ninth hole where I was 4-up, I took it a bit easy and just wanted to make regulation pars and wait for him to make the mistake," said Pratap.
A missed putt on the fourth cost him the hole. However, he made a birdie on the very next hole to draw level.
After a keen fight, Sajib hit a wayward second shot and ended up with a bogey to lose the hole.
Sajib then made a birdie on the 11th to go 1-up and won the next hole with a par to increase his lead.
However, things turned around in the next three holes as Karan won all of them, thanks to a shaky putter of Sajib.