The Dutch were denied a victory in their the World Cup Group F opener when Koki Ogawa’s 88th-minute header took a deflection off Daichi Kamada before going in at the AT&T Stadium in Dallas.
After a drab first half where chances were few and far between, the came to life when an unmarked Virgil van Dijk headed home in the 51st minute from Liverpool team-mate Ryan Gravenberch’s cross.
Netherlands’ lead lasted just six minutes as Takefusa Kubo passed to Keito Nakamura, who drifted outside the area before rifling low into the net via a ricochet from Jan Paul van Hecke.
Ronald Koeman’s side went ahead again in the 64th minute when Crysencio Summerville cut in from the right on to his weaker left foot, ignoring the overlapping Denzel Dumfries, and firing excellently beyond Japan goalkeeper Zion Suzuki and in off the post.
Japan threw caution to the wind after going behind a second time, with head coach Hajime Moriyasu introducing all five substitutes.
And the move was vindicated as they started to pen back their opponents before the equaliser came in the closing moments.
A corner from Junya Ito saw fellow substitute Ogawa rise highest in the area and his header took a final telling touch from Kamada, with Dutch goalkeeper Bart Verbruggen only able to parry into his net.
Netherlands captain van Dijk said: “They didn’t create that much, so that’s why it’s extra disappointing that we conceded through a set-piece. But that’s the reality, we take the point, and now we focus on Sweden.
“We just have to keep going. Hopefully there are still many more games to come for us. Because we conceded late on, it doesn’t feel as nice, but we move on.”
Japan coach Hajime Moriyasu admitted the point was “a little disappointing”.
“We managed to get a result through our collective effort,” he said. “We defended patiently and then tried to be more aggressive going forward. The players executed what we had planned and prepared for.”