Daichi Kamada deflected a header from Koki Ogawa into the net in the 88th minute to reward the fighting Samurai Blue in a pulsating match in Dallas, Texas on Sunday.
Captain Virgil van Dijk headed the eighth-ranked Dutch ahead in the 51st minute and Crysencio Summerville restored the lead in the 64th with a classy shot into the far left corner.
Japan had levelled for the first time from Keito Nakamura's low shot in the 57th as the game came to live after the break following a more cagey first half.
The Japanese maintained their unbeaten streak even though the draw ended a run of six victories, including against Brazil and at Wembley against England. They had also not conceded in five matches until Liverpool's van Dijk ended that run.
They are considered dark horses and finally want to win a knock-out match after four last-16 defeats when they got out of the group. In 2022 they beat Germany and Spain in the group before losing on penalties against Croatia.
"Unfortunately we didn't win today but we will do that in the next game (against Sweden)," player of the match Van Dijk said.
Coach Ronald Koeman regretted that his team let a lead slip twice but said the draw was OK "based on the chances at both ends. I thought it was a top-class match, so you can be happy with a draw."
The Dutch are three-time finalists and went out on penalties in the quarter-finals against eventual champions Argentina in 2022.
Ronald Koeman's side started well with a third-minute chance from Donyell Malen whose shot was saved by goalkeeper Zion Suzuki, who also saved a header from the Dutch forward in the 37th.
In-between Hiroki Ito aimed high, Nakamura shot just wide in the 43rd and Feyenoord Rotterdam's Ayase Ueda hit the side-netting.
The goals came after the break. Oranje drew first blood after Japan had cleared a free-kick as Ryan Gravenberch's cross found Van Dijk at the far post to nod home.
The joy was short-lived as Nakamura found the left corner from the edge of the penalty area six minutes later.
Another seven minutes on Gravenberch found Summerville who cut inside from the right and curled his first national team goal into the far corner in Arjen Robben fashion.
Suzuki made a big save against Cody Gakpo before the Japanese mounted the pressure in the closing stages. Bart Verbruggen saved well from Sugawara but in the 88th Ogawa's header bouncing of Kamada's head went in off his gloves.
The other teams in the group are Tunisia and Sweden who meet later on Sunday at the Mexican venue of Monterrey.
