Pak, who led Sorenstam by three shots going into the last round of the 54-hole event, shot a 1-over 73 to finish at 7-under 209, one stroke in front of Sorenstam, who had a closing 71.
A year ago, Sorenstam shot a 66 to come from 10 shots behind leader Pat Hurst on the final day, then beat Mi Hyun Kim on the first hole of a playoff.
Sorenstam sent the tournament down to the wire again this time, with a birdie on the 17th hole to draw within one shot of Pak, who bogeyed the hole.
But Sorenstam's winding 30-foot birdie try on No. 18 curved just past the hole, then Pak's birdie putt from 20 feet stopped one rotation short of the cup, leaving the 24-year-old to tap-in for par and the win.
The victory, worth $150,000 of the $1 million purse, was her 14th since she joined the LPGA Tour in 1998.
Laura Diaz shot a 73 to finish third at 3-under 213. Kelli Kuehne had a 68, Jackie Gallagher-Smith a 70, and Wendy Doolan a 72 to tie for fourth at 215.
Sorenstam hurt her chances when she bogeyed the 160-yard, par-3 16th. She left her tee shot short of the green, but pitched within three feet of the hole. After Pak missed a 10-foot birdie putt, Sorenstam's short putt for par rimmed the cup and came out - dropping her three shots behind Pak with two holes to go.
Pak had made a 15-foot birdie putt on No. 13 to open a two-shot lead, as Sorenstam left a long birdie try eight feet short of the cup, but made the putt for par.
Sorenstam, who said she wanted to get off to a fast start on Sunday, didn't, with pars on the first three holes. Instead, she got some help from Pak, who bogeyed both the par-4 second and third holes.
Sorenstam drew even with a birdie on the fourth hole, then moved ahead with another birdie on No. 5 as Pak had pars on both holes.
Just as quickly, Pak shifted the momentum back her way, making birdie putts on the next two holes to pull into a tie, then going back in front with a par 3 on No. 8 while Sorenstam bogeyed.
Leading by a shot, Pak missed a chance to go up by two when her 8-foot birdie putt on the ninth hole slipped just past the edge of the cup. Exasperated, Pak flipped her putter into the air like a baton and caught it.
She and Sorenstam, who two-putted from the fringe, each settled for par on the hole and headed into the back nine separated by one shot.
Sorenstam had won two of the four earlier events she played this year, including defending her title in the year's first major, the Kraft Nabisco Championship.
Pak's win at El Caballero was her first of 2002.
Sorenstam tied Mickey Wright's 37-year-old LPGA record for overcoming the biggest final-round deficit in a victory when she won the 2001 Office Depot.
Full-field scores from The Office Depot Championship Hosted by Amy Alcott