Sneijder's 53rd-minute strike finally broke down Japan's stubborn resistance, which had stifled Dutch creativity for much of the match. Robin van Persie laid the ball back and Sneijder sent a powerful right-foot shot that Japan goalkeeper Eiji Kawashima could only deflect into his net.
"We pressed in the second half and got a goal," Sneijder said. "This is the kind of game we maybe could have got two or three goals, but we won it and that's great." It was the Inter Milan playmaker's 15th goal in 63 internationals.
"Our players did everything they could, but we could not beat the Netherlands," Japan coach Takeshi Okada said.
"We feel sorry for the fans." The Netherlands, however, again failed to live up to its billing as one of the most fluent attacking teams of the tournament. The team struggled to a 2-0 victory over Denmark in its first Group E match, while Japan had a 1-0 victory over Cameroon.
"Why do we focus on good football instead of winning?" Netherlands coach Bert van Marwijk said. "Let me assure you that we really, really want to win and if we can do that in style then great. But you have to be able to win ugly games." Before Sneijder's goal, Van Persie missed chances for the Dutch in front of 62,010 fans at Moses Mabhida Stadium.
Japan responded to the goal by pushing forward and Yoshito Okubo had two shots in quick succession, the first saved by Netherlands goalkeeper Maarten Stekelenburg and the second went over the bar.
Substitute Ibrahim Afellay came close to doubling the Dutch lead in the 84th and again in the 88th when he bore down on the Japan goal, but he was foiled both times by good saves from Kawashima diving at his feet.
Japan nearly made the Netherlands pay for those misses when substitute Shinji Okazaki latched onto a deep cross at the far post and shot just over the bar.
"It shows you there are no easy games. Look at France and Germany," Van Marwijk said, referring to the World Cup losses for the European powerhouses.
The Netherlands reached the World Cup final in 1974 and 1978, but lost both times. Japan's best finish was reaching the round of 16 when it co-hosted the tournament with South Korea in 2002.
The win set a record of 10 straight victories for the Netherlands in World Cup qualifiers and final tournament matches, including eight before the two in South Africa.
It also extended the Dutch record of never losing to an Asian team. It has now won eight matches and drawn one against Asian opponents.
The win put the Netherlands in first place in Group E with six points. Cameroon and Denmark are also in the group.
Van Marwijk said he was expecting an aggressive Japan team and that's what he found as Okada played a four-man defense and a mobile five-man midfield that never gave the Dutch time to settle on the ball.
The Netherlands dominated possession early with Rafael van der Vaart, Dirk Kuyt and Van Persie all switching positions across the midfield to confuse Japan's defense.
Kuyt had the most spectacular Dutch effort before the break, with an overhead kick in the 10th minute after a cross from Giovanni van Bronckhorst, but defender Yuji Nakazawa headed the effort clear.
A minute earlier, Sneijder had also came close with a free kick that flashed over the bar.
But after soaking up the pressure, Japan came back into the game and created its own scoring chances.
Keisuke Honda headed over in the 33rd after a free kick from Yasuhito Endo, and Marcus Tulio Tanaka did the same five minutes later when he climbed above Kuyt but could not direct his header down.
As Japan continued to push forward, Stekelenburg easily saved Daisuke Matsui's volley and Honda sent a long-range free kick harmlessly over the bar.
But after the break, Japan struggled to regain its momentum, allowing the Netherlands to again dominate possession and finally find a way to the goal.
Maarten Stekelenburg, Gregory Van der Wiel, John Heitinga, Joris Mathijsen, Giovanni Van Bronckhorst, Mark Van Bommel, Nigel De Jong, Wesley Sneijder (Ibrahim Afellay, 83), Rafael Van der Vaart (Eljero Elia, 72), Dirk Kuyt, Robin Van Persie (Klaas-Jan Huntelaar, 88).
Eiji Kawashima, Yuto Nagatomo, Yuji Nakazawa, Marcus Tanaka, Yuichi Komano, Makoto Hasebe (Shinji Okazaki, 77), Daisuke Matsui (Shunsuke Nakamura, 64), Yuki Abe, Yasuhito Endo, Keisuke Honda; Yoshito Okubo (Keiji Tamada, 77).
