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.
However, a clumsy lunge from Yasuyuki Konno in the Japan box allowed Colombia the chance to open the scoring, and Juan Cuadrado made no mistake from the spot.
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 defender 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.