Stenson was an incredible nine shots clear of the elite field midway through the third round at East Lake, with the first prize of 1.4million US dollars and 10million bonus for winning the FedEx Cup seemingly a certainty.
But the world number six stumbled home in 38 as the rain which had forced tee-times to be brought forward by several hours duly arrived, a round of 69 leaving him 11 under par.
American Dustin Johnson carded an excellent 67 to move into second place on seven under, with compatriot Steve Stricker a further two shots back after a 68.
US Open champion Justin Rose is four under alongside Zach Johnson, Jordan Spieth and Billy Horschel, with former world number one Luke Donald another stroke adrift after matching Johnson's 67.
Birdies on the second, third, seventh and ninth had taken Stenson to 14 under par - he is 13 under for the front nine this week - nine shots ahead of Dustin Johnson.
But that lead fluctuated wildly on the back nine with bogeys from Stenson on the 10th and 14th, coupled with birdies from Johnson on the 15th and 16th cutting it to five shots.
A birdie on the 15th took Stenson six shots clear again but driving into a fairway bunker cost the former Ryder Cup player another shot on the 16th and three-putting the 18th from 45ft gave the chasing pack a glimmer of hope going into the final round.
"I've got to take the positives still," Stenson told Sky Sports. "It was tough conditions on the back nine and I hit a couple of wayward shots and it's hard to find your rhythm again when you are out in very much European conditions.
"The only one which stings a little is the three-putt on the last; I hit a very nice first putt and looked like I almost made it but missed the one coming back. I still have my four-shot lead and I'm going to go out and try to play well again.
"I lost my feel a little bit on the back nine, hopefully we have a nice day tomorrow and I can start in the same form as I have the other rounds."
As one of the top five in the FedEx Cup standings coming into the event, Stenson knew that victory on Sunday would guarantee him the massive bonus payment.
And having lost a reported seven-figure sum in the Ponzi scheme run by disgraced financier Allen Stanford, the jackpot would be very welcome.
"[It is] not all my money, but I have quite a big part of my own savings and investments with them," Stenson said when the scandal broke. "It's a very unfortunate situation. I'm a victim as everybody else in that big thing."
Speaking after his second round on Friday, Stenson added: "It's a personal matter, but I'm not struggling by any means. For me, it's more important to leave here with two trophies. I mean, at the end of the day, it's just money, isn't it? I care more about the two trophies than I do the 11 million, that's for sure."
Johnson scraped into the Tour Championship in last place in the standings and needs Stenson to finish in a three-way tie for sixth or worse to claim the FedEx Cup title as well.
"I'm playing solid," he said. "I've played pretty good every day not doing anything really crazy, getting a lot of looks at birdies and this is definitely the best I have played on this golf course.
"Tomorrow I just need to go out and do exactly what I've been doing. My year this far has been a little up and down but it's starting to turn. I feel like I am starting to play a bit better."
Masters champion Adam Scott had been Stenson's nearest challenger but felt ill overnight and was put on an IV drip in the clubhouse before play got under way.
The Australian's coach Brad Malone told the PGA Tour website: "He was tired last night and had a restless night of sleep. Hopefully it was just a quick bug. He feels considerably better than he did when he first got here."
Scott struggled to a 74 to lie nine shots off the lead on two under, while world number one Tiger Woods carded a 69 to be 26th on three over.