Scott opened with rounds of 69 and 67 at the Yokohama Country Club then wound back the clock with a six-under 65 that left him just one stroke off the lead at the start of Sunday
But the 46-year-old former world No.1 failed to extend his golden run, with a double bogey on the 13th proving the low point of a one-over 72.
Scott finished five strokes behind American winner Michael Brennan, who also carded a six-under 65 on Saturday but backed it up with a composed three-under 68 on Sunday.
The 2013 Masters winner will be deeply frustrated, having put together some eye-catching rounds since finishing ninth at this year's British Open.
Fellow Australian Min Woo Lee finished on a high with a five-under 66 to grab a share of ninth spot, but was left to lament his third round of 72 that made it effectively impossible to win.
Brennan finished 16-under 268 for the tournament, parring the final six holes to remain one stroke clear of fellow Americans Keith Mitchell and Jacob Bridgeman.
It was Brennan's second victory of the season and third on the PGA Tour.
"It was an unbelievable week," Brennan said, having rebounded from a bogey on the 10th with birdies on holes No.11 and 12.
"I was very nervous today, especially coming down the stretch. Jacob and I had a great battle ... and that was really fun. We played a lot of golf in college together.
"Japan was spectacular. The fans were amazing this week. It was so awesome to have my brother fly out here and be here for the weekend.
"I was frustrated after 10, probably could have handled it a little bit better ... but making a really nice roll on 11 and 12 was huge."
Jordan Spieth, making his first start of the FedEx Cup Fall, tied for 13th at 11 under after a 67, while Japanese star Hideki Matsuyama, the 2021 winner, tied for 21st.
The PGA Tour's lone stop in Asia featured its strongest field of the FedEx Cup Fall series, with Scott among a group of 13 Presidents Cup players who took part.
With AP
