The two leaders, dressed in dark suits and ties, presented wreaths and bowed their heads in silent respect during a brief tour of the USS Arizona Memorial that commemorates the US sailors and Marines who perished on the battleship on December 7, 1941.
According to the local reports, three people have been injured, two of them critically in the shooting incident in which the suspect gunman took his own life.
The return of the US servicemen's remains was part of a deal that was agreed to by Trump and Kim back in their summit in June.
Thousands observed a moment of silence and watched jets streak across the clear blue sky at a ceremony at Pearl Harbor marking the 75th anniversary of the attack that plunged the United States into World War II and left more than 2,400 service people dead.
Curtains will fall on the Rim of the Pacific 2016, the world's largest international maritime exercise, on August 4.