An Augusta native seeking his third PGA TOUR victory and first since the 2007 Nissan Open, Howell had a 13-under 203 total on at TPC Sugarloaf.
Perry shot a 69. David Toms (69), Ryan Palmer (70) and second-round leader Jonathan Byrd (73) were two strokes back at 11 under.
With storms expected Sunday afternoon, the players will tee off in threesomes, starting on both the first and 10th holes. Howell, Perry and Toms are set for 10:15 a.m. on No. 1.
It will be different, Howell said. Its not the normal twosomes later in the day. From what I understand, its going to be quite windy. This golf course is really tough in the wind. Theres a lot of risk-reward out here. A lot of it.
Ryuji Imada, who finished second to Zach Johnson in playoff last year, shot a 66 to tie Heath Slocum (69) or sixth and move within three shots of the lead.
Howell has held three leads after 54 holes, but finished second each time.
On the four par 5s, Howell leads the field at 10 under with birdies Saturday at Nos. 6 and 10. He eagled the sixth hole Thursday.
Avoiding temptation to go for corner pins was important to Howell, who describes the Greg Norman-designed Sugarloaf as favoring him because it doesnt demand so many drivers off the tee.
There is some strategy and thought off the tees as well as into the greens, Howell said. Thats why I think its so important to get the ball in play off the tee. There are slopes in these greens, and you can use them to help you go to the flags, but youve got to have the ball in play.
Perry seems fully recovered from an 81 in the final round last week at The Players Championship. He was just one shot off the lead after 54 rounds at TPC Sawgrass before windy conditions and faulty irons wrecked his weekend.
Imada and Justin Bolli (68) are both former University of Georgia standouts seeking their first tour victory. Bolli is in eighth place, four shots back.
Omar Uresti, one of four players tied for ninth and five strokes off the lead, had a tournament-best 65. Brett Quigley (68), Steve Elkington (68), Craig Kanada (69) and Camilo Villegas (71) also were 8 under.
Byrd led the field by three shots after two rounds, but he dropped three strokes to 9 under with three bogeys through his first eight holes.