The gold went to 24-year-old Italian, Alex Schwarzer, who finished in 3 hours 37.09 minutes and the silver to Jared Tallent of Australia, whose time was 3 hours 39.27 minutes.
The Italian also broke the Olympic record of 3 hours and 38.29 minutes, previously held by Vyacheslav Ivanenko of Russia.
Nizhegorodov, who took silver at the 2004 Olympics in Athens and is the holder of the current world record (3 hours and 34.14 minutes), said the bronze medal was not what he was expecting to win at the Olympics.
"I feel very disappointed. I don't know why. I don't think I had any technical problems or mistakes. I got a silver four years ago, but now it's only a bronze. It's such a pity," the official Olympics website quoted Nizhegorodov as saying.
With two days left of Olympic competition, Russia is currently ranked 4th in the overall medal standings with 16 gold, 16 silver and 20 bronze medals, while China tops the standings, boasting 46 gold, 15 silver and 22 bronze medals.