Colombia striker and captain Radamel Falcao, who is 32, played in the first World Cup match of his career but failed to extend his all-time scoring record of 29 goals for Colombia.
His teammate, midfielder Carlos Sanchez became the first player of the 2018 FIFA World Cup to be shown a red card after handling the ball inside the penalty area early on.
Colombia equalized through Juan Quintero's free-kick in the 39th minute after goal-line technology confirmed that Japan goalkeeper Eiji Kawashima only grabbed the ball behind the line.
Yuya Osako nodded in second-half substitute Keisuke Honda's corner in the 73rd minute to secure Japan's victory.
Poland will take on Senegal in the other Group H match, set to be played in Moscow later on Tuesday.