When Kelly stepped to the par-3 fourth hole, he was two shots behind Els, who looked like his smooth-swinging, Big Easy persona during the first two rounds. But Kelly stunningly caught his playing partner with a 4-iron shot that hit the green, bounced to the flag stick and dropped in.
And Kelly wasn't done.
He tapped in for birdie on the next hole to move in front, then added two more birdies to extend the lead to two shots. When Kelly knocked in an 8-footer for birdie on the 12th hole, he was three strokes ahead of the field.
Kelly finished with a 67 and, at 13 under, stood a stroke ahead of Els (71), who drained a 35-foot birdie putt on the 18th hole, and Kevin Na (66).
Masters winner Zach Johnson kept up his inspired play after his emotional, draining triumph at Augusta National. His 66 left him four shots back along with Stephen Ames (64), Vaughn Taylor (67), Sean O'Hair (69) and Stephen Leaney (70).
Els seemed ready to end his nearly three-year PGA Tour victory drought and cap a lengthy comeback since knee surgery in 2005. He made only one bogey the first 36 holes, his two 65s leaving him a shot off the tournament's halfway scoring mark.
But Els was off target from the start Saturday. He drove right into some trees on the first hole, then struck a tree with his next shot. His third landed in a bunker and Els ended with a double-bogey 6. He steadied himself two holes later with a birdie that pushed him two shots in front of Kelly - and set up Kelly's dramatic ace.
After the tee shot went in, Els high-fived Kelly, who raised both arms in celebration. When Kelly pulled the ball from the cup, he gestured to throw it into the gallery before abruptly stopping and shaking his head "No,'' a big smile on his face.
"Not many times things go the way you plan them,'' Kelly said. "That went in the way I planned it.''
It was the 12th ace at the Verizon Heritage, which has been played on Harbour Town Golf Links since 1969.
Kelly's three-shot margin disappeared with a pair of bogeys on the 13th and 15th holes. But he regained the lead when Els had more tree problems, this time on the 16th. Els drove behind the large tree on the right side of the fairway. His approach struck the branches and landed about 50 yards away, leading to a bogey.
Johnson continued to show he wasn't out of game after his big victory and three days of celebrations and celebrity meetings. He shot a 66 - improving by two strokes for third straight round - and had a chance to become the first Masters winner to follow with victory here since Bernhard Langer in 1985.
Johnson didn't spend much time practicing since gaining the green jacket. After all, there were TV appearances like David Letterman to make and dignitaries like presidential candidate Barack Obama to meet. So Johnson called on last week's momentum to keep him going here. "I still feel the good vibes from last week,'' he said.
Divots: Ames' 64 was his best round of the year, surpassing a 67 last month in the second round of the Arnold Palmer Invitational. ... Threatening weather led organizers to move back Sunday's tee times to 11 a.m. with groups of three going off the first and 10th tees. ... Overheard along the third hole, a spectator from the Northeast talking of Sunday's impending storm: "Enjoy the snow. Make sure you plow my driveway.'' Harbour Town was expecting severe thunderstorms forecast for overnight and early Sunday morning.