Drained of energy, the Australian needed an intravenous drip just to start his third round at East Lake and was unable to play at his best.
The Masters champion shot five over par for his first nine holes to quickly tumble down the leaderboard and although he improved on the back nine, it was too little, too late.
His third round 74 left him tied for 10th place, nine shots behind runaway leader, Henrik Stenson, and with virtually no hope of claiming the $10 million jackpot on offer at the season-ending event.
"I wasn't feeling top drawer last night and had a rough night," Scott said.
"I had fever throughout the night and not a lot of sleep. It was uncomfortable and I didn't feel too flush this morning, so I had to get some help. I feel a lot better now, but it was pretty rough this morning.
"The way I was feeling this morning, without the doc's help, I definitely wouldn't have been going. I was really flat and not in a good way. Hopefully I can rest up tonight and feel better tomorrow."
Asked whether he was suffering from stomach flu or a head cold, Scott replied: "It's a bit of both. It's nasty. I don't feel 100 percent, but I feel okay, good enough to get around. I started feeling good with about four holes to go."
Scott's ailment could not have come at a worse time as he was only four strokes behind pacesetting Stenson overnight and had been playing good golf.
The Australian, like Stenson one of just five players in this week's field of 30 who would automatically guarantee FedExCup honours by winning the Tour Championship, had oozed self-belief after shooting a 69 on Friday.
Less than 24 hours later, that upbeat mood had been wiped out by his night of flu and fever. His third round included three bogeys, a double bogey and a lone birdie.
"Yeah, I'm pretty disappointed because I felt like I could have made a run today with some good golf," said Scott.
"It went completely the other way. When your body's feeling so lethargic and heavy, the club feels like it weighs 60 pounds, and it was just hard work to get anything moving.
"All your rhythm and everything is off when your body is feeling so poor. You know, it was a battle for me today, and I'm disappointed that I wasn't at 100 percent to try and give Henrik a shake and stick with him."
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- Henrik Stenson