With 10 minutes to go Japan were losing 1-0, but with Colombia leading Senegal by the same scoreline in the other simultaneous Group H tie it meant Japan would qualify on fair play with Colombia.
Senegal defeated Poland 2-1 in their opening game and twice led Japan before settling for a 2-2 draw that left both countries with four points.
Down to the final day of group play in the World Cup, things can get tricky in trying to determine which teams are moving on to the knockout stage, and which are going home.
This marked the first time in World Cup history that a team progressed out of the group stage via their Fair Play record.
After the game, Pekerman told reporters he was anxious about the condition of the 26-year-old, who spent last season on loan at Bayern Munich from Real Madrid, while also attempting to play down the situation given Colombia's qualification for the last 16.
"I think we could have scored a goal in the first half", Cisse said. Starting at this year's tournament, disciplinary records - known as fair play - were added by Federation Internationale de Football Association as a tiebreaker. Japan also got some grief for finishing its game just knocking the ball back and forth in the real-life version of the famous scene from The Simpsons ("midfielder holds it ... holds it ... holds it").More news: Clippers Trade Austin Rivers To Wizards For Marcin Gortat
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Colombia coach Jose Pekerman said he was "extremely concerned" for James Rodriguez after he limped off during their win over Senegal.
Gary Lineker, analysing the highlights of the match following Colombia's win over Senegal, echoed the sentiments of most football fans by saying: "This surely goes against what the game stands for".
Michael O'Neill, Northern Ireland manager and BBC pundit: "It takes you back to World Cups in 1982 and 1986, when we saw games like that".
Japan has reached the knockout round at the World Cup three times in the last five tournaments.
Colombia manager Jose Pekerman has admitted he is anxious about star player James Rodriguez, the Bayern Munich forward was substituted in the 31st minute of their final group game against Senegal on Thursday.