For Japan, the defeat has confirmed their exit from the Brazil tournament as they finished bottom of the group.
Here, Sports Mole takes a closer look at the match.
On target: 7
On target: 4
Was the result fair?
Despite Japan's superior possession and shots statistics, it was a fair result as Colombia were by far the more threatening in the final third. Japan had a chance to go on and dominate at the start of the second half but they let their opponents come back at them, while Colombia seemed to get stronger as the match progressed. They scoreline seems a little harsh, but the Colombia win was certainly justified.
Japan kept the ball well and certainly played positive football for much of the game, but often looked hurried while in the penalty area, and were too easily stretched at the back by Colombia. They did seem to tire in the final 10 minutes, allowing the South American side the run up the score and end their chances of a comeback to book a place in the last 16.
Colombia made a quiet start to the match, but made the most of their opportunities, converting all four on their on-target efforts into goals. The side appeared to get stronger and more commanding as the match went on, with James Rodriguez and Jackson Martinez making a formidable partnership in the final quarter of an hour.
Sports Mole's man of the match
James Rodriguez: He may have only played half of the match, but James Rodriguez's impact in the second half of the match turned the result around. Colombia could easily have let Japan take the lead after their late equaliser in the first half, but Rodriguez provided a threat from the moment he was introduced, and set up one of Martinez's goals as well as scoring one of his own in the final minutes.
This honour goes to Japan defender Yasuyuki Konno for conceding a penalty in the 16th minute of the match. As a result, Colombia were able to take the lead through a Juan Cuadrado spot kick. Japan had been in control of the match until then, and things could have turned out very differently if they had not had to spent most of the game trying to come from behind.
Portuguese Pedro Proenca had a relatively solid game, correctly awarding Colombia a penalty early in the game before rightly waving away a couple of shouts later in the tie. Eder Balanta may have been fortunate to escape punishment for an elbow on Shinji Okazaki, but it was not clear how intentional his actions were, so a decent performance on the whole from Proenca.
Japan: With this defeat confirming their exit from the tournament, Japan will next be in action in September when they are due to play a series of friendlies in preparation for next year's Asian Cup.
Colombia: This win ensures that they finish top of Group C, setting them up with a match against Uruguay on Saturday.