Just as their opening game, a 2-0 win over Denmark, Bert van Marwijk's side failed to cut loose, but recorded another important victory.
Japan pressed hard and got men behind the ball but had no response to Sneijder's thumping drive shortly after half time.
The Dutch controlled possession from the start but were unable to find a way through the resolute Japanese during a dogged first-half performance.
Sneijder drilled a free-kick over the bar and wasted another set-piece but the Dutch were well stifled.
In fact, the Japanese also enjoyed the better chances of the opening period, with the Netherlands giving away countless free kicks around their area.
Keisuke Honda flashed a header wide from a free-kick from Yasuhito Endo, who also created an opportunity for Marcus Tanaka.
After a fine breakaway, Daisuke Matsui had a stinging drive held by Dutch goalkeeper Maarten Stekelenburg and Honda fired over with yet another free kick.
The Netherlands emerged with greater purpose after the interval and Robin van Persie passed up a couple of openings.
The Arsenal man headed straight at Eiji Kawashima from Giovanni van Bronckhorst's cross and then scuffed wide from a fine ball from Mark van Bommel.
But seven minutes after the restart, the Dutch took the lead with a strike of real quality.
Van Persie laid the ball off for Sneijder and the Inter Milan midfielder drilled a shot with enough power to beat the 'keeper.
The impressive Yoshito Okubo threatened with a couple of efforts from distance as Japan were forced to alter their defensive game-plan.
As Japan pressed and pressed, Gregory van der Wiel had to pull off a desperate clearance to deny Honda.
The Dutch almost doubled their lead when Eljero Elia fed Ibrahim Affelay but goalkeeper Kawashima rushed out to make a fine block.
Kawashima was called into action again when Klaas-Jan Huntelaar played through for Affelay only for the goalkeeper to make another solid save.
But Japan wasted their best chance to equalise when Shinji Okazaki lashed over in added time.
Netherlands (4-3-3): Stekelenburg; Van der Wiel, Heitinga, Mathijsen, Van Bronckhorst; Van Bommel, De Jong, Sneijder (Afellay 83); Kuyt, Van Persie (Huntelaar 88), Van der Vaart (Elia 72). Subs (not used): Robben, Boulahrouz, Ooijer, Braafheid, Vorm, Schaars, Babel, Boschker, De Zeeuw.
Japan (4-5-1): Eiji Kawashima; Komano, Tanaka 8, Nakazawa, Nagatomo; Abe, Endo, Hasebe (Okazaki 77), Matsui (Nakamura 64), Okubo (Tamada 77); Honda Subs (not used): Narazaki, Kawaguchi, Uchida, Daiki Iwamasa, Konno, Morimoto, Inamoto, Kisho Yano.