Japan are still without a point from four outings in the round-robin league, but were pressing for an equaliser when the rain-disruption encounter against Pakistan came to an end.
Pakistan, who placed one foot in the semifinals with this victory, now have six points from four games with a fixture against China remaining.
In the encounter that featured two breaks for a total of 40 minutes due to torrential showers, Pakistan took the initial lead in the fifth minute through Muhammad Ifran Jr open field strike.
Attacking in unison, Japan breached the Pakistan defence to draw 2-2 parity in the last minute of the first half through a flash strike by Kenta Tanka.
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Pakistan's third goal came through the quick-silver reflexes of Muhammad Rizwan Sr. Following the deflection from a Japanese defender in a packed circle, Rizwan Sr stretched to reach the ball and sent a snap reverse shot into the citadel, surprising goalkeeper Genki Mitani with his shot from the narrow angle.
Bilal scored his second panalty corner goal in the 52nd minute to make it 4-2, but Pakistan defence faced some late pressure from Japan.
Hirotaka Zendana converted a penalty stroke in the 54th minute to bring Japan within one goal of Pakistan's score, but failed in their effort to score another goal during the last five minutes.