Entering the event a day after claiming the 10m pistol bronze, Rai upped the ante as the final closed in on the elimination rounds.
The unassuming Army-man shot a total of 230.1, a world record, to finish on top of the podium, while Amanpreet, who was leading for a major part of the final, had to be satisfied with the silver after aggregating 226.9.
The 29-year-old Rai was placed sixth at the end of the first two competition series of five shots each with 93.8. At that point, Amanpreet was leading the eight-man field with 98.9.
The Punjabi shooter extended his domination with a series of high scores, even as Rai tried to make his way back into contention after a start that included a horrendous 6.6, much to the disbelief of the partisan crowd.
A stunning 10.8 in one of the elimination rounds proved to be crucial for Rai, who jumped from sixth to the third position, and knocked out Kazakhstan's renowned marksman Vladimir Issachenko in the following round with a 10.5.
After upstaging Golkhandan, Rai comfortably got the better of Amanpreet in the gold medal round, finishing the event with an excellent 10.5 to lay his claim on the top prize.
"It's amazing to win this gold medal here during the first combined World Cup held here in India, in front of my supporters. It's a great honour and a true emotion to see the Indian flag atop the podium," said Rai.
(REOPENS DEL 37)
Earlier in the qualification round, Amanpreet had led the charts with 561 points while Jitu was second with 559 points. They had finished first and second respectively in the qualification stage.
In the day's other events, Indian shooters failed to qualify for the finals. In women's 25m rapid fire pistol, Muskan finished 12th with 576, while Rahi Sarnobat was way behind at 23rd.
In women's skeet, Rashmee Rathore ended 17th, Arti Singh Rao was 24th and Saniya Sheikh was 27th in the qualification stage.
Prior to today's results, Pooja Ghatkar had won the host nation its first medal -- a bronze -- on day one of the competition, Ankur Mittal had bagged the trap silver with Rai claiming a bronze in the 10m air pistol event.
Thailand's Naphaswan Yangpaiboon won the gold medal in women's 25m rapid fire pistol event with a score of 38.
China's Jingling Zhang (30) bagged silver, while Michelle Skeries (27) ended with a bronze, both prevailing in shoot-offs.
In women's skeet, USA's legendary Kimberly Rhode clinched the gold medal with a world record score of 56, while Thailand's Sutiya Jiewchaloemmit (51) won silver and Chloe Tipple (42) of New Zealand ended with bronze.