Lorie Kane carded a 70 to take third place at 6-under-par 138. Lorena Ochoa and Brittany Lincicome were next at 5-under-par 139.
Sorenstam had her streak of five straight victories on the LPGA Tour end last week at Kingsmill, but the Swede seems ready to put that behind with another stellar round at Eagle's Landing Country Club.
'I love being on the leaderboard,' said Sorenstam, who is seeking her 60th career victory on the LPGA Tour. 'I love being out there and having a chance to be competitive on Sunday. I strive for that. That's what keeps me going and I'm not afraid for the challenge.'
Sorenstam dropped a wedge inside 7 feet for a birdie at the par-5 second and reached the green in two at the par-5 sixth. She two-putted for a birdie to move to 7 under and played her approach to 6 feet for a birdie at the par-4 10th.
The 34-year-old kept on rolling with a birdie at the par-4 12th and tapped in for another birdie at the par-5 13th. Sorenstam then knocked her second shot within 8 feet of the hole at the par-4 14th and ran home the birdie try to make it three in a row.
Sorenstam was cruising down the stretch with three straight pars before her second shot to the par-5 closing hole came to rest 5 feet from the cup. Sorenstam drained the eagle putt to complete her back nine in 30 and take a commanding advantage into the weekend.
'I'm very, very pleased,' said Sorenstam. 'I thought I played very good today, especially on the back nine. To finish with an eagle is obviously a nice feeling.'
Bowie started on the back side and rolled in a 30-foot putt for a birdie at the par-4 14th. Bowie was on the green in two at the par-5 18th and took two putts for another birdie.
The 30-year-old found trouble with a bogey at the third, but responded with a birdie at the very next hole after her tee shot to the par-3 fourth stopped 30 feet from the cup. Bowie drained the putt and landed her second shot in a bunker at the par-5 sixth. Bowie hit her third shot out to 10 feet and sank the putt en route to a round of 69.
'Six shots is a lot on anyone when you are that far back,' Bowie said of the prospect of catching Sorenstam. 'She could very well go out and shoot 64 again tomorrow. All I can do is try and go out there and play better than I played the first two days because I cannot do anything about what she is doing.'
Beth Daniel, Candie Kung, Jeong Jang, Emilee Klein and Sung Ah Yim share sixth place at 4-under-par 140. Last week's winner, Cristie Kerr, was one shot further back at 3-under-par 141 alongside Karrie Webb, Candy Hannemann, Michelle Estill and Aram Cho.
Defending champion Jenny Rosales finished in a tie for 38th at even-par 144 after a round of 76.
The 36-hole cut fell at 2-over-par 146 with 72 players qualifying for the weekend. Among those less fortunate were: Laura Diaz, Rosie Jones and Paula Creamer.