Thomas, who won five times this season and claimed his first major at the PGA Championship, carded a closing 66 to lose by a stroke to rookie Schauffele, who birdied the final hole for a 68 and finished at 12-under-par 268.
"It’s a really weird day, getting asked what it’s like to win the FedExCup because as a competitor you’re mad you didn’t win the tournament," Thomas said in a greenside presentation.
"What an unbelievable honour this is, the fact that you can win something over the course of an entire year.
"I played really well all season and it was nice to play well in some playoff events finally and have it all pay off.
"It was a gruelling day for sure and nerve-racking. Xander is a deserving champion (of the Tour Championship) and I’m glad to walk away with this (FedExCup)."
Thomas started the 2016-17 season last October with a victory on the other side of the world in Kuala Lumpur, Malaysia, before adding two wins in Hawaii, the PGA Championship in North Carolina and the Dell Technologies Championship in Massachusetts.
He credited his hot form to an improved short game, the result, he said, of hard work.
Thomas also won the PGA of America Player of the Year, which is based on a points system for tournament wins, official prize-money and scoring averages.
Spieth, the 2015 FedExCup champion, had a chance to lift the trophy for the second time in three years, but a tie for seventh at East Lake was not enough to stave off Thomas.
He finished second in the standings, collecting a $3 million consolation prize, while Schauffele jumped to third and picked up a $2 million bonus on top of his Tour Championship prize money of $1,575,000.
"This was my worst putting week of the year, unfortunately, but what a great season it was," said Spieth, who won three times including his third major title at the British Open.
"J.T. (Thomas) obviously is very well deserved to win the FedExCup this year. It is rightfully so given his season.
"The progression that he has made this year into becoming such a tremendous closer has been phenomenal to watch.”
Thomas and Spieth will team up on the United States team against an underdog International side at the Presidents Cup in New York starting on Thursday.
"I’m very pleased with the way 2017 has gone and we have a chance to cap it off next week in New York,” Spieth said.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Toby Davis/Ian Ransom)
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