World Championship silver medallist Rai shot 235.1 to comfortably finish top of the podium.
Mitharval, who had established a new qualification games record with 584, eventually finished with the bronze medal after aggregating 214.3 in the eight-man finals at the Belmont Shooting Centre.
Australia's Kerry Bell secured the silver medal with 233.5, having managed to topple Mitharval from the second position.
In the finals, Jitu started on a strong note and led with 100.4 at the end of stage 1, while Mitharval was third with 98.1.
In stage 2 elimination, Rai started with 10.3 and 10.3 to lead the pecking order, even as his compatriot moved up and displaced Bell at second place with two 10.1s. Championship
Rai continued to surge ahead with a 10.2 but an 8.4 disturbed his momentum somewhat, as the next shot fetched him 9.2.
Meanwhile, Mitharval closed the gap as Rai had just 8.8 in the 18th shot to Mitharval's 10.0.
Last month, the young Indian shooter had combined with Manu Bhaker to claim the mixed team air pistol gold in the ISSF World Cup in Guadalajara, Mexico.
And he displayed that form today too, en route to creating a new qualification record. He competed well the finals too, but came up short against a rampaging Rai, a winner of multiple gold medallist in top global events.
Mitharval slipped even as Rai managed another 10.0 and maintained the lead throughout to emerge triumphant.
Such was Rai's lead that scores of two 9.2 in the last two attempts did not matter in the end. That Kerry managed a low 8.6 in his final shot also did not help his cause and the gap only widened.
In the qualifying, Mitharval equalled the Commonwealth Games record of 584 on his way to qualifying for the final.
Mitharval had a series of 96 96 98 99 96 99, while Jitu's sequence read a strong 98 to start with followed by 92 94 96 95 95.
In the finals though, the show belonged to Rai, a CWG gold medallist in 50m air pistol event four years ago in Glasgow and the 2016 World Cup Finals' 'Champion of Champions'.
In 2017, Jitu won four gold medals and a bronze at ISSF events and two bronze medals at the Commonwealth Shooting Championships.