Furyk (68), Howell (67) and Owen (69) were tied at 7-under 135, a stroke ahead of a group that included two-time Verizon champ Boo Weekley and Stuart Appleby.
Choi, who played alongside Tiger Woods all four rounds at Augusta National Golf Club, opened with 64 on Thursday. However, he couldn't maintain that pace and fell three shots off the lead after 74 at Harbour Town Golf Links.
"Yeah, the fatigue is setting in right now," said Choi, who tied for fourth with Woods last week. "But no excuses today; I had a tough time reading the greens."
Furyk didn't have Choi's problem entering Harbour Town.
"I didn't play enough to get tired," he said about Augusta, where he missed the Masters' cut for just the second time in 14 appearances.
On Friday, Furyk stuck approach shots within 10 feet on the 13th and 15th holes for birdies. He caught Choi for the lead when he chipped in from just off the green on No. 16.
Furyk, whose round ended just as Choi teed off, expected the South Korean to continue the strong play from last week, when he tied for fourth at 11-under with Woods.
Choi, though, quickly fell back when he drove out of bounds on No. 11, then put a tee shot in the water on No. 14, both for bogeys.
After a double-bogey 6 when he failed to get out of a bunker on No. 18, Choi trailed by three. He held things together with an even-par final nine to remain in contention.
"I'm not that far behind," said Choi, seeking his first PGA Tour win since 2008.
Howell tied Furyk with a birdie on No. 18 where the late afternoon roared through the course's signature lighthouse hole. He rolled in a 22-footer from off the green.
"Sometimes it's better to be lucky than good," he said.
Owen moved to 7-under after putting his approach on the par-5 fifth hole within two feet for birdie, then parred out the rest of the way.
Weekley posted his second 68, the first time all year he opened with two sub-70 rounds.