Maika Hamano scored the decisive goal in the 17th minute, turning five metres outside the box and firing the ball past diving Australia goalkeeper Mackenzie Arnold and into the corner of the net.
Australia's Matildas, Asian champions in 2010, gave as good as they got in a high-quality final and ultimately paid the price for their inability to convert the chances they created.
Record goalscorer Sam Kerr was well shackled inside the penalty box and her fellow striker Caitlin Foord failed to make the most of a string of chances.
The Nadeshiko were forced into desperate defence in the final 10 minutes as Australia, roared on by the largest crowd in Women's Asian Cup history, poured forward in search of an equaliser.
Substitute Emily van Egmond had two shots blocked and Alanna Kennedy's header from Ellie Carpenter's cross was well saved by Japan goalkeeper Ayaka Yamashita.
Former world champions Japan, playing in their seventh Asian Cup final, held on to add another Asian title to their 2014 and 2018 triumphs.