But the ball finally disappeared after circling the cup, leaving Schauffele with a wide smile of relief on his face.
“My hands were shaking so much, I was so nervous,” world number 66 Schauffele said at the victory presentation.
“I was very embarrassed. I don’t want to win with a huge all-round lip-in.”
Schauffele carded a closing 68 to finish at 12-under-par 268, while Thomas shot 66 to claim second-place on 11 under.
The performance clinched for Thomas the FedExCup, and a $10 million bonus, awarded to the winner of the season-long points race.
Thomas overtook Jordan Spieth, who started the Tour Championship as points leader. Spieth finished equal seventh in the tournament and slipped to second in the FedExCup standings.
He received a $3 million consolation prize, while Schauffele finished third in the standings.
It was a fairytale finish to the season for 23-year-old Schauffele, who barely qualified for the 30-man Tour Championship field.
“It’s been a wild ride. I weaseled my way in,” he said as his father Stefan looked on.
Stefan was a promising German decathlete whose international dreams were dashed when he suffered a serious eye injury in a car crash.
He subsequently moved to the United States and married a woman from Taiwan, the couple settling in southern California.
“I’m so happy he’s here and I can share it with him,” Schauffele said of his father.
Schauffele broke out of a tight five-way battle, after five players had been bunched within one stroke on the back nine.
He made a fine up-and-down par save at the penultimate hole after a deft chip to remain tied with Thomas, before another precise chip at the par-five 18th set up his winning putt.
Russell Henley (65) shot the day’s best score to tie for third with fellow American Kevin Kisner (70) at 10-under, while Englishman Paul Casey finished another shot back.
Overnight leader Casey (73) did not make a birdie until the final hole.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Toby Davis)