With this victory, the American also increased his lead over Anand to 8-2 in personal encounters apart from 13 draws in Classical games.
Anand, who turned 47 on Monday, slipped back to 50 per cent score while Nakamura reached the same score with his first victory in the tournament.
With six rounds still remaining in the super tournament, Wesley So continued to lead the tables on 2.5 points after escaping with a draw against Levon Aronian of Armenia.
Aronian, Russian Vladimir Kramnik and Fabiano Caruana of United States share the second spot now on two points each while Anand, Nakamura and Anish Giri of Holland share the fifth spot on 1.5 points, a half point ahead of French Grandmaster Maxime Vachier-Lagrave.
Michael Adams of England and Veselin Topalov of Bulgaria share the ninth spot with a half point each.
After three decisive games each in round one and two, the day witnessed just one game providing the decisive result.
Anand went for the Ragozin in the Queen pawn opening by Nakamura and the American deviated from an earlier game by the Indian to get some attack with his white pieces.
Anand sacrificed his queen for two pieces but was unable to create a fortress as Nakamura was spot on. The American did not slip up in the complexities.
Wesley So put up stiff resistance against Aronian in one of the most interesting games of the day. The Filipino-turned American is having the best time of his life on the chess board and this game was another extension that saw him come out unscathed in a difficult situation. In the end Aronian managed to only enter a drawn endgame.
Veselin Topalov had similar opportunities against Vachier-Lagrave but in the end the Frenchman also found defensive resources to steer the game to a draw. It was a well-played game by Topalov and the Bulgarian was not happy with his efforts.
Results (Round 3):
Hikaru Nakamura (Usa, 1.5) beat V Anand (Ind, 1.5); Levon Aronian (Arm, 2) drew with Wesley So (Usa, 2.5); Michael Adams (Eng, 0.5) drew with Anish Giri (Ned, 1.5); Maxime Vachier-Lagrave (Fra, 1) drew with Veselin Topalov (Bul, 0.5); Fabiano Caruana (Usa, 2) drew with Vladimir Kramnik (Rus, 2).
Image: Viswanathan Anand