First-half goals from Hikaru Naomoto and Aoba Fujino put the Japanese in a commanding position in front of 6,992 at Dunedin Stadium.
The scoreline would have been larger were it not for the heroics of Costa Rica goalkeeper Daniela Solera, who kept her side in the contest against a Japanese side who registered 25 shots to their 6.
Providing heavyweights Spain beat minnows Zambia in Wednesday's later game in Group D, Japan will advance to the knockout stages for a fourth straight World Cup.
Solera was able to frustrate them for large parts of the game as her side slumped to a successive defeat.
The Costa Rica No.1 held onto a Saki Kumagai header and parried a Naomoto effort wide as her side found themselves on the wrong end of a high-octane start from the Japanese.
There was only so much Solera could do and when rightback Maria Coto slipped giving chase to a ball, Japan had their opening.
Coto's stumble allowed Naomoto to get to the ball first and the experienced midfielder was on hand to fire in for a 25th-minute opener.
More misery was on its way for Costa Rica when Fujino found space on the Japanese right and charged into the box two minutes later.
The 19-year-old Japanese forward could have passed but unleashed a shot at Solera's near post instead and it paid off beautifully with the No.1 unable to keep the powerful effort from going in at a tight angle.
Japan continued to threaten until half-time but the Costa Rica goalkeeper kept them at bay.
The Costa Rica stopper did well to prevent efforts from Honoka Hayashi and Yui Hasegawa going in during the opening quarter of an hour of the second half.
With victory assured Japan took their foot off the gas.
Coach Futoshi Ikeda took off both goalscorers in the latter period of the second half knowing next Monday's game against Spain in Wellington will likely decide who tops the group.
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