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.
England managed only two shots on goal and earned just 47 percent of possession.
By accumulating fewer yellow cards than Senegal did, Japan qualified for the round of 16.
Nishino said he passed on clear instructions to the rest of the team when he sent on midfielder Makoto Hasebe as a second-half substitute - no risks and no yellow cards.
Japan and Senegal wound up with four points apiece when their World Cup group's final games finished, sending it to a new Federation Internationale de Football Association tiebreaker rule to determine who advanced to the knockout stage. Colombia topped the group with six points.
This means that Japan ended the tournament level with Senegal on four points.
The only goal of the game came in the 75th minute when Mina rose like a spire amidst the Senegalese penalty area to ram home Juan Quintero's corner.
Meanwhile, Colombia can be proud of its World Cup 2018 turnaround.
Aliou Cisse's team finished with the same number of points, same goal difference and goals scored as their Asian rivals in Group H - the first three deciders of ranking in the pools.
Colombia beat Senegal 1-0 to top World Cup Group H on Thursday. This tiebreaker is making its debut at the 2018 World Cup.
Poland's star striker Robert Lewandowski missed a good chance to double the lead in the 74th minute, meaning he failed to score in all three matches he played at the World Cup in Russian Federation.
The match was often lethargic anyway in the 36°C (96.8°F) heat, but the stupor was broken at the 59th minute when Poland's Rafał Kurzawa floated a free kick to the far post and an unmarked Jan Bednarek scored from close range. He was the Whoscored.com Man of the Match with an 8.45 rating.
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