Rodriguez's stunning goal against Uruguay in the second round, when he controlled the ball with his chest and volleyed home from distance, was one of the tournament's best moments.
Colombia kicked things up another gear, with James coming alive in the search for an equaliser, but the Japanese defence proved equal to the task.
Colombia is in now serious danger of failing to advance out of group play with games against Senegal and Poland.
I like Sanchez a lot, but compared to toby he is miles away, just pay Toby the going rate?
What was Jose Pekerman doing?
Colombia continued to rally but the effect of playing with 10 men for nearly the entire game took its toll with Japan holding out, leaving Colombia with a mountain to climb in Group H.
The onus will now be on Colombia's all-time leading goalscorer Radamel Falcao to lead the frontline in his absence. Subs: Barrios 5, James 4, Bacca 5. As for Japan, Shinji Kagawa starts as the number 10. Subs: Honda 7, Yamaguchi 6, Okazaki 6. Sanchez blocked Shinji Kagawa's shot with his extended right arm and was ejected.
He will now try to help Colombia overcome the barrier of being down to 10 men after Carlos Sanchez was sent off at 3 minutes.
While Carlos Sanchez took the fall, namesake Davinson was equally at fault as he allowed a ball over the top to bounce in the build-up to the penalty incident, giving Osaka a chance to shoot and Kagawa the opportunity to pounce on the follow-up.
Midfielder Carlos Sanchez was dismissed for a deliberate handball as Colombia went 1-0 down in the opening stages of the clash at the Mordovia Arena in Saransk. Colombia are in a situation.
So here are ten stats you might have missed from Japan against Colombia. Clever clever! I love this game! The goal was confirmed by goal-line technology. Inui thinks about fouling him but somehow manages to refrain, gets nowhere, and Japan attack again.
Though the rest of the team performed admirably after that to keep themselves in contention of pulling off a battling result, they came up just short. David Ospina had come for the cross, leaving a big target for Osako, but the header was perfectly placed into the corner. Ospina, obviously, is nowhere.
It took 18 attempts, but finally an Asian team have triumphed over the perennial World Cup achievers of South America, with the former continent suffering 14 defeats during that time.
Colombia was one of the stories of the last World Cup, with James Rodriguez rising to prominence with his performance in Brazil. The record is now P18 W1 D3 L14.