A point was enough to see Honduras through in second place, setting up a Wembley quarter-final clash with Brazil, while group winners Japan will play Egypt at Old Trafford.
Neither side were able to take the initiative in a dull first half, with Honduras closest to breaking the deadlock.
Three-goal striker Jerry Bengtson exquisitely chested the ball down and beat his marker in the same movement before testing Japanese keeper Shuichi Gonda with a placed effort across goal.
Gonda also did well to tip away Maynor Figueroa's free-kick, which took a huge deflection en-route to goal.
Target man Kenyu Sugimoto's header was cleared late on and Yuki Otsu's jinking run ended in a weak shot on goal for Japan.
The second half also lacked the action a boisterous crowd deserved with neither side showing much intent on goal until a late spell of pressure from the Japanese.
Honduras keeper Jose Mendoza palmed over a Manabu Saito free kick that thratened to float into the top corner ten minutes from time, and recovered well to keep the same man away from a driven Kensuke Nagai cross.
Jose Velasquez also stepped in at just the right moment to tackle Otsu when well placed.