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.
Japan midfielder Shinji Kagawa stepped up to convert the ensuing penalty and put his side in front six minutes into the match.
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.
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