Zoeller and Jacobsen won six skins at the two-day event and earned $320,000.
The 2007 winning duo of Jack Nicklaus and Tom Watson finished second after Nicklaus missed a 12-foot birdie putt at No. 18 in regulation. A make would have given the team its second straight Skins game victory.
The second-place finish was worth $270,000.
"It's a crazy game and things were just falling our way," Zoeller joked. "Guys were missing putts and we had an opportunity to make a couple to get us into the positive category and it just blossomed from there."