The Samurai Blue had beaten Colombia and drawn with Senegal to enter its final Group H match, against already-eliminated Poland, requiring only a point to reach the last 16.
But Japan scarcely threatened as Shinji Kagawa and Takashi Inui started on the bench and it was instead dependent on results elsewhere after Jan Bednarek's fine strike won the game for Poland.
Colombia's Yerry Mina came to Nishino's rescue, though, as his goal defeated Senegal and ensured Japan progressed in second place due to their superior disciplinary record.
Senegal's six yellow cards to Japan's four ultimately cost the African side, which exits Russia in disappointing circumstances.
On this showing, neither England nor Belgium – Japan's potential last-16 opponents – will fear playing Nishino's men, who will be grateful simply to make the knockout stages and may well be unrecognisable after this risky experiment.