India's only Olympic gold medallist in individual sport, the 32-year-old Bindra shot a total of 208 to walk away with the top prize and defend his title in 10-metre air rifle at the Balewadi Shooting Range.
Vijay, a silver medallist at the 2012 London Games, shot a total of 571 to become the new national champion in 25-metre standard pistol category.
Bindra had revealed his decision to only train twice a week just before the 2014 Asian Games in Incheon where he won a bronze.
Ironically, Rajput had taken the pole position in the qualifications shooting a total of 624, while Bindra trailed the Haryana marksman by 3 points.
Also Read
In the team event the Army Marksmanship Unit of Satyendra, Chain Singh and Chavanke Ashok won the gold medal shooting 1857.5 points. Punjab finished second with a total of 1846.3 and the Air Force team settled the bronze with a total of 1842.9.
In the 25-metre standard pistol event, Army marksman Gurpreet Singh walked away with the silver medal after shooting 570. Omkar Singh from Navy settled for the bronze with a total of 568.