Nestruev went into the 10-shot final two points adrift of South Korean soldier Jin Jong-Oh, who might have taken the title himself had he not blown it with his seventh bullet.
Jin was left with the silver after that 6.9 score left him with a mountain to climb against a determined opponent who sealed victory with a final 10.6 flourish into the bullseye.
Nestruev's final score of 663.3 points was 1.8 clear of Jin's 661.5, with North Korean Kim Jong-Su finishing third with 657.7
The Russian had taken the lead after the fourth shot of the final, surrendering it again after the sixth before Jin's decisive lapse under pressure that brought a gasp from spectators.
Bulgarian veteran Tanyu Kiriakov, the defending champion from Sydney four years ago, failed to repeat the feat and finished seventh.
Russian soldier Boris Kokorev, the 1996 Olympic champion, was fifth.