Stenson was an incredible nine shots clear of the elite field midway through the third round at East Lake, with the first prize of $1.4m and a $10m bonus for winning the FedEx Cup seemingly a certainty.
But the world No 6 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 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 - nine shots ahead of Johnson. But that lead fluctuated wildly on the back nine with bogeys 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 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 for today's final round.
Stenson said: "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."
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 started.
The Australian's coach, Brad Malone, said: "Hopefully it was just a bug."
Scott struggled to a 74 to lie nine shots off the lead on two under, while Tiger Woods carded a 69 to be 26th on three over.