India will face Belgium in the quarter-final.
India opened the scoring with SV Sunil netting one in the third quarter.
Netherland's Mink van der Weerden scored the equaliser in the 36th minute to make it 1-1.
Manpreet Singh extended the lead in the 47th minute for India and then Rupinderpal Singh's drag-flick off a penalty corner in the 49th minute of the game made it 3-1.
Netherlands reduced the gap with Weerden scoring another in the 58th minute to make the scoreline finally look 3-2.
In the other clashes of the day, Argentina beat Germany 3-0, Australia defeat Pakistan 3-0, England drew against Belgium 1-1.
England has topped its Champions Trophy pool.
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