Manavjit qualified for the final round after shooting 122 with a series of 25,24,24,25 and 24 and was a point below the qualification round leader Daniele Resca (123) of Italy.
The 34-year-old Indian missed two birds in the final but held his nerve to hit the remaining 16 targets to grab the gold with a point's margin. His total final score was 145 (122+23).
Manavjit had recently won gold in the Commonwealth Shooting Championships at Delhi with a score of 146 (124+22).
"I did not realise that I was going to win until the last shots. It has been a very close competition. I just won by a single target. I shot aggressively up until the end and eventually made it to the top," Manavjit said from Acapulco.
"It was a long trip here from India but it was worth it. I am planning to take part in most of the ISSF World Cup stages, this year," added the 2006 World Championship gold medallist.
Another Indian, Anirudh Singh also impressed by entering his first ever World Cup final with a score of 122.