The LPGA Player of the Year matched Debbie Massey's 36-hole record in this event with an 11-under-par 133. She owns a two-shot lead over Laura Davies, who vaulted up the leaderboard on Saturday with a 7-under-par 65.
Sorenstam began the round tied for the lead with Marisa Baena but fell behind early thanks to a birdie at one by Baena and a pair of birdies by Woo-Soon Ko. The Swede quickly rebounded with a birdie at No. 3 and took sole possession of the lead with a birdie at No. 5.
The Swede found herself tied for the lead at 8-under par with Davies and Ko but after she eagled the par-5 9th, she took a two-stroke lead.
It turned out to be a lead that would stick as no player made a move up the leaderboard. Davies birdied the last to get within one of Sorenstam, but after the seven-time winner on tour birdied the par-5 16th, the lead was two.
Sorenstam has sewed up Player of the Year honors and the money list title. If she hoists the trophy on Sunday, she will earn $106,000 and be less than $10,000 away from becoming the first player in LPGA Tour history to break the $2 million plateau in one season.
Davies, who won this year's Wegman's Rochester International, made her move on the front nine at Musashigaoka Golf Course. She collected birdies at Nos. 1 and 3 and added birdies at the final three holes to go out at 5-under 31.
She made only two birdies the rest of the way as she sits at 9-under and in the best shape to stop Sorenstam from winning both titles on the LPGA Tour's Japan swing as the Swede won last week's World Ladies Match Play Championship.
Yuri Fudoh and Kayo Yamada share third place at 8-under par. Fudoh, who reached 9-under before a bogey at No. 17, carded a 68 while Yamada shot a 69 on Saturday.
Baena birdied No. 1 to tie for the lead but managed pars the rest of the way for a 71 and fifth place at minus-seven.
Ko posted a double-bogey and a bogey on the back to drop into a tie for sixth with Jean Bartholomew, Aki Takamura and Yu Ping Lin at 6-under-par 138.
Defending champion Lorie Kane rebounded from an opening-round 73 with a 3-under 69 on Sunday. The Canadian is tied for 22nd at minus-two.
This event combines 42 LPGA Tour players and 35 members of the Japan LPGA Tour. It is a 54-hole tournament with no cut.
Full-field scores from the Mizuno Classic