The former champions booked their spot in the tournament for the first time since 2022.
The Green Shirts made a rampant start to the high-stakes fixture, with captain Ammad Butt opening the scoring in just the ninth minute, courtesy of a sensational field goal.
Pakistan's early lead remained intact until the culmination of the first quarter and was eventually neutralised in the 21st minute when Ryoma Ooka scored a field goal for Japan.
Japan took control of the match in the penultimate quarter as Shota Yamada and Koji Yamasaki struck in quick succession to bolster their lead to 3-1.
But Pakistan made a sensational comeback in the final quarter, netting three goals through Abu Mahmood, Sufyan Khan and Afraz in the 52nd, 55th and 57th minutes, respectively, to reclaim the lead.
Both teams went all out in the dying minutes of the game, but Pakistan's defence held its nerves to retain the lead until the final whistle.
Notably, the victory marked Pakistan's fourth consecutive victory in the ongoing FIH Hockey World Cup 2026 Qualifiers as the Green Shirts capped off the group stage unbeaten.
Pakistan kicked off their campaign with a narrow 5-4 victory over China, powered by a brace from Rana Waheed.
A dominant 5-3 win over Malaysia followed, before they rounded off the group stage with a resounding 4-2 triumph over Austria, with Abu Mahmood netting twice.
Pakistan will face England in the final of the qualifying event, scheduled to be played at the same venue on Saturday.