Narang, who won bronze at this Olympics, finished 20th and Rajput was further down the standings at 26th as they failed to qualify for the final at the Royal Artillery Barracks.
Narang finished with a score of 1164 while Rajput had 1161. Top eight qualified for the final. Italian Niccolo Campriani set an Olympic record of 1180 to take top position in the qualification round.
The 29-year-old Narang had given India its first medal in London. He took bronze in the 10m Air Rifle event. He also failed to make the cut in 50m Rifle Prone.
With this, Narang's campaign in this Olympics has ended.
Rajput, the 31-year-old, too finished his stint in London on a disappointing note. This was the only event he was participating in, and he has failed to progress further from the qualification stage.
Scores of Gagan Narang and Sanjeev Rajput in qualification
Prone: Rajput 395/400 (98, 98, 99, 100)
Narang 398/400 (100, 99, 100, 99)
Standing: Rajput 378/400 (96, 95, 91, 96)
Narang 377/400 (97, 90, 96, 94)
Kneeling: Rajput 388/400 (98, 96, 97, 97)
Narang 389/400 (97, 97, 98, 97)