Sorenstam played in one of the later groups on Friday and waited until the end of her round to make a move up the leaderboard. She started her climb to the top with a birdie at the par-four 14th but matched Baena for first with birdies at her final two holes at Musashigaoka Golf Course.
The LPGA Player of the Year is hoping to sweep through the two-event Japanese swing on the LPGA Tour. Last week, she bested Se Ri Pak in the final of the Cisco World Ladies Championship for her seventh win of her amazing 2001 campaign.
Baena opened on the back nine at Musashigaoka Golf Course and picked up four birdies on her front side. She posted four pars in a row at the start of her second nine but caught fire starting at the fifth, as she rattled off three consecutive birdies to get to seven-under par.
The 24-year-old from Colombia bogeyed the par-three eighth hole to drop to six-under and after a par at No. 9, she finished with 66 and a piece of the first-round lead.
France's Patricia Menuier-Lebouc and Yuri Fudoh share sixth place with four- under-par 68s, followed by Wendy Doolan and Yu Ping Lin, who are knotted in eighth at minus-three.
LPGA Tour competitors Laura Davies, Silvia Cavalleri, Grace Park and Karen Weiss are part of the logjam tied for 10th at two-under par.
Defending champion Lorie Kane and Sophie Gustafson, whom she bested in a playoff last year, are seven off the pace after one-over rounds of 73.
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