India, who lost 2-5 against Japan in the pool stage, scored two eye-catching field goals to register a narrow win in Asia Cup, Super 4s.
Both India and Pakistan finished on four points each in Pool A but the defending champions qualified for the Super 4s on better goal difference.
Ken Nagayoshi, Kosei Kawabe, Ryomi Ooka and Koji Yamasaki scored for Japan while Pawan Rajbhar and Uttam Singh found the target for the Indians.