An Augusta native seeking his third PGA Tour victory and first since the 2007 Nissan Open, Howell had a 13-under 203 total 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 this 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. "It's not the normal twosomes later in the day. From what I understand, it's going to be quite windy. This golf course is really tough in the wind. There's 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) for sixth, three shots behind Howell.
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 Sugarloaf as favoring him because it doesn't demand so many drivers off the tee.
•Ochoa up by 2: Two-time defending champion Lorena Ochoa shot a 5-under 67 and left retiring Annika Sorenstam in her wake after two rounds of the rain-shorted $2 million Sybase Classic in Clifton, N.J.
Ochoa enters today's final round of the now 54-hole tournament with a 9-under 135 total and a two-shot lead over third-year tour player Teresa Lu and veteran Sophie Gustafson. South Koreans H.J. Choi and Na Yeon Choi — no relation — are three behind.
Brittany Lang was four back, and Sorenstam, who announced Tuesday that this would be her final year on the LPGA Tour, was five behind after a 1-over 73 that included a double bogey after hitting a tree on a par 5, and a bogey on her final hole.
•Bean leads Champions: In Hoover, Ala., Andy Bean birdied the final hole to take a one-shot lead over Mike Goodes heading into the final round of the Regions Charity Classic with two of the top Champions Tour pl
