The game began with the Japanese on the front foot, pushing forward in a bid to unsettle their opponents, with Yoshito Okubo providing the first concrete chance of the game as he curled the ball just wide in the 10th minute.
The South Americans had another penalty appeal turned down when Jackson Martinez fell in the area, but the referee waved play on.
The 2002 World Cup co-hosts, however, had several chances to equalise, most notably in the 27th minute when Shinji Kagawa rounded two defenders before unleashing a strike which had to be saved by the opposition keeper.
The levelling goal duly came right on the stroke of half time, when Keisuke Honda sent a dangerous ball to the middle of the area and Shinji Okazaki connected with his head to power beyond David Ospina.
Colombia, already assured of passage to the second round, weren't to be thwarted by their opponents, and duly took the lead again when James Rodriguez drove a pass through the Japan backline to allow Martinez to strike with a low-angled shot into the corner.
The duo combined again to allow Martinez to fire home once again eight minutes before the end, while Rodriguez was also able to get on the scoresheet in injury time after turning Maya Yoshida inside out and smashing the ball into the net.
Colombia are through to the knockout stages with a maximum nine points from nine, while Japan are knocked out with a solitary point from their three group games.