Kate Golden shot a 65 to finish alone in third at 9-under-par 135, while Rosie Jones and Penny Hammel were one stroke farther back at 8-under-par 136.
Sorenstam was two shots off the pace to start the round but the lead was never out of sight. She nabbed her first birdie of the day at the par-3 second where she hit an 8-iron off the tee to nine feet and made it two in a row with an 18-foot birdie at the very next hole.
The Swede two-putted for birdie at the fifth and ran home a 30-footer for birdie at the following hole. At the par-5 seventh, Sorenstam chipped inside eight feet for her third consecutive birdie.
Sorenstam was equally as effective on the inward nine at Columbia Edgewater Country Club with an eagle at the par-5 10th. She then drained a 20-footer for birdie at the par-5 12th and hit a sand wedge within 11 feet of the cup for a birdie at the 14th.
At the par-3 16th, Sorenstam dropped a 6-iron three feet from the hole. The 31-year-old made the birdie putt to complete her best round of 2002.
'I think I feel as good as my score,' said Sorenstam, who set a new course record. 'I feel great obviously. Today it seems like I always knew what to hit. Seldom in between clubs. I was never in trouble really. The longest par putt I had was probably two or three feet.'
Sorenstam returned to the LPGA Tour after a short break with a victory at last week's Williams Championship. She is 18 holes away from making it two in a row and adding to an outstanding season.
'I played really solid,' said Sorenstam. 'Some days when you struggle it's complicated, you're always between clubs, you're in the rough instead of the fairway, but today it was a green light all day long.'
Stupples picked up three straight birdies on the front nine to make the turn at 7-under. She continued her fine play on the back nine with three birdies over the first five holes but ran into trouble with a bogey at the par-3 16th after she couldn't get up and down from off the green.
The 29-year-old responded well at the 18th after she hit a wedge to 25 feet and drained the putt for her seventh birdie of the day and a round of 66.
'I'm really excited about how I played today,' said Stupples. 'I was pretty nervous starting out the day but I made a few birdies and that really settled me down nicely.'
Jamie Hullett and Heather Bowie finished six shots back in a tie for sixth at 7-under-par 137.
Karrie Webb and Juli Inkster, who were tied for the lead after round one, were one shot farther back after matching 71s. The duo was joined by Beth Bauer, Laura Davies, and Kelly Robbins at 6-under-par 138.
Mi Hyun Kim, who won this event in 2000, carded her second straight round of 71 to finish in a tie for 36th at 2-under-par 142.
The 36-hole cut fell at 1-over-par 145 with 88 players qualifying for the final round.
Full-field scores from the Safeway Classic