The Netherlands started brightly and nearly took an early lead when Donyell Malen met a pass from Cody Gakpo, but Japan goalkeeper Zion Suzuki reacted well to keep the effort out. Japan responded with a threatening attack of their own, only for Jan Paul van Hecke to produce an important challenge to deny Daizen Maeda.
Chances remained limited during a tightly contested first half. Malen again tested Suzuki with a header, while Micky van de Ven headed over from a dangerous delivery. At the other end, Keito Nakamura and Ayase Ueda both went close as Japan finished the half strongly.
The breakthrough finally arrived six minutes after the restart. After a partially cleared free-kick, Ryan Gravenberch delivered an excellent cross into the box and captain Virgil van Dijk powered a header in off the post to put the Dutch ahead.
Japan responded almost immediately. Just six minutes later, Takefusa Kubo found Nakamura, who drove forward before firing a low shot that took a slight deflection and beat Bart Verbruggen at his near post.
The match continued at a high tempo and the Netherlands regained the lead in the 64th minute. Making his first appearance at a major international tournament, Crysencio Summerville produced a superb left-footed finish into the far corner to restore the Oranje advantage.
However, Japan refused to give in. Kubo remained a constant threat and nearly equalised with a powerful long-range effort before the Blue Samurai struck late. In the 89th minute, substitute Koki Ogawa met Junya Ito's corner with a header that deflected off Daichi Kamada and beyond Verbruggen to secure a valuable point.
Netherlands coach Ronald Koeman defended his tactical decisions after seeing his side surrender the lead twice.
"There was also a problem with pressure on the flanks. If you look at both goals, we didn't defend well," Koeman said.
"Football is a funny game because after Japan scored the second goal, they started defending as well. We could have scored a third goal. So I don't regret my choices."
Koeman admitted his side had not reached their usual standards and insisted improvement would be needed as the tournament progresses.
"Of course we can perform better and we need to grow during the tournament," he said. "This definitely was not our best performance. Of course, we would have preferred to win the first game. We expected to."
Japan coach Hajime Moriyasu praised his players' determination but revealed he was still disappointed not to leave with all three points.
"The Netherlands were very strong, a very difficult opponent, but the players were united as one," Moriyasu said. "They fought to the end and did not cease to persevere."
"We were aiming to get three points, not one point. In that respect, it was a little disappointing."
The Dutch will next face Sweden in Houston, while Japan take on Tunisia in Monterrey on June 20.