The inaugural Points Plane will also have a special inflight service including a unique cocktail and meal service, signature pyjamas and inflight giveaways.
Should the initial trial prove successful, the program could be extended to other destinations.
Qantas CEO of Loyalty, Olivia Wirth told Sunrise that Japan was chosen as the first location due to its popularity.
"It's one of our top five searched destinations online so we know it's going to be a hit," she said.
"We're trialing this as a new way for our customers to use their points. Let's see how it goes!"