Ritsu Doan scored a 71st-minute winner for Japan after New Zealand's Ben Old cancelled out Ayase Ueda's opener in the first half.
Japan are looking to win the Asian Cup for the first time since 2011 when the tournament kicks off in Saudi Arabia in January.
Their win over New Zealand in front of over 60,000 fans at Tokyo's National Stadium saw them lift the Kirin Cup, after beating Ecuador on penalties in the semi-finals last week.
Panama beat Ecuador 7-6 on penalties after a 1-1 draw in the third-place match earlier in the day.
Japan also beat Uruguay and Venezuela at home in this international window.
The matches were their first since being eliminated by Brazil in the last 16 at the World Cup in North America.
Japan had several early chances to take the lead against New Zealand, with forward Doan causing havoc in the opposition's defence.
Ueda eventually made one count just before the half-hour mark, slotting home from close range for his fourth goal in four games.
New Zealand looked like they could be in for a long evening, but instead they hit straight back when Old pounced for the equaliser four minutes later.
Japan pushed for a winner in the second half, and New Zealand goalkeeper Alex Paulsen denied Ao Tanaka with a fantastic acrobatic save.
But the home team stuck to the task and were rewarded when Doan swept home another slick passing move.
Japan have been drawn in a first-round group with holders Qatar, Thailand and Indonesia at the Asian Cup.
It will be coach Hajime Moriyasu's last tournament in charge before he hands over to the incoming Go Oiwa