Nanjappa shot a series of 97, 96, 95, 99, 97, 96 to top the round with 580 points and make the final scheduled later today.
However, Om Prakash missed out by a point after shooting series of 93, 97, 92, 95, 95, 96 to total 568.
England's Stewart Nangle (578) came second while Daniel Repacholi (574) of Australia took the third spot in the qualification round.