But the Spaniard ended up plummeting to last, losing places hand over fist after pitting to change the medium tyres he started on for softs and ultimately making a second stop.
Following analysis back at Nakajima Racing's Gotemba factory, the reason for Palou's dramatic loss of pace was traced to an intercooler tube that had become loose and tangled up inside the car's right-rear suspension.
This had the effect of blocking airflow to the diffuser, costing Palou an estimated 70kg of downforce - causing his laptimes to plummet and his tyres to wear out faster.
Speaking to Motorsport.com, Palou said: "The team made a super-good stop and I said, 'That's it, we have this', because the rhythm was not in doubt.
"And suddenly in the second lap [on the softs], I saw that I could not go at the rhythm; I was slower than I was with the mediums, which had never happened to us.
"I started losing two, three, five seconds per lap... five or six cars passed me, I went back to the pits to change and changing [tyre] pressures, but the championship was lost. The same thing happened again with another set, which was almost new.
"I'm sad, really, because we have always had the rhythm and I saw it possible to be champion. I just had to win the race and after the first stop it was won. Suddenly, everything vanished in a moment, but this is racing and sometimes these things happen to you."
Palou concluded his rookie campaign third overall with a single victory at Fuji, helping Nakajima Racing to third in the teams' standings behind Dandelion Racing and TOM'S.
Third in the championship: Alex Palou, Nakajima Racing