A point was enough for both teams to progress to the next round going into the match, but the Samarai Blue have pipped the Central Americans to first place.
Takashi Sekizuka's men had already sealed their place in the quarterfinals, but went into the match knowing that defeat to the Hondurans would consign the team to second place. Honduras meanwhile, knew that a mere point would see it through thanks to an unlikely victory against Spain on matchday two.
It was Luis Suarez's men that started the brighter of the two sides, immediately setting out in pursuit of an early goal shortly after kickoff and winning a series of corners, none of which came to fruition.
However, while the Central Americans were lively going forward, their Asian opponents were looking dangerous. Gotoku Sakai made an excellent interception on the quarter-hour mark and wasted no time in spraying the ball to Yuki Otsu, who strode forward and unleashed a shot straight at Jose Mendoza.
At the other end, Anthony Lozano superbly brought the ball forward from his own half, dodging a series of challenges, but could only direct a long-range strike high and wide under pressure from a number of defenders.
Manabu Saito went on a mazy run through the Honduras half, only to drag an effort well wide, before Sakai drove narrowly wide of Mendoza's goal, while Kenyu Sugimoto had a header blocked at point-blank range by Johnny Leveron.
Five minutes from the break, though, it was Luis Fernando Suarez's side which had the best chance of the half. Jerry Bengtson, the hero of his side's previous two fixtures, superbly brought down a high ball on his chest, shrugged off his marker and prodded a shot towards goal that Shuichi Gonda did well to block.
Maynor Figueroa forced another save from the FC Tokyo goalkeeper soon afterwards with a driven free kick that took a heavy deflection off a Japanese body, ensuring a stalemate going into the interval.
As at the start of the first half, both teams began the second period at a good pace, but found it desperately difficult to cut out any clear-cut chances.
Sugimoto had an ambitious effort easily saved by Mendoza, but in truth, neither goalkeeper faced any real challenges for much of period after the break.
Honduras was happy to concede free kicks to hamper Japan as it looked to set up camp in midfield, and on one occasion, the team almost paid for it.
Anticipating a cross, Mendoza crept off his line as Takashi Usami lined up a free kick on the left wing. The former Bayern Munich winger over hit his delivery, forcing the 23-year-old keeper to pedal backwards and acrobatically tip the ball over his bar.
Another Usami set piece found Kazuka Yamamura at the far post, but Mendoza managed to dive to his right to stop the 22-year-old's goal-bound header.
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