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.
It was the Inter Milan playmaker’s 15th goal in 63 internationals.
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.
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.
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.