Shakeel Abbasi and Rehan Butt scored for Pakistan.
India's Sandeep Singh converted two penalty corners while Dharamvir Singh scored a field goal in India's victory.
India will face Japan in their last league match on Sunday.
India beat Pakistan 4-1 at the World Cup in March, won 4-2 in the Azlan Shah tournament in Malaysia in May and hammered the rivals 7-4 at last month's Commonwealth Games.