Daly and Holmes, two of the PGA TOUR's longest hitters, played the final seven holes of the alternate shot format at 7 under par, making five birdies and an eagle to join Leonard and Verplank in the lead.
In the alternate shot format, the teammate whose drive is not used hits his team's second shot, and they alternate shots until the ball is holed.
Holmes ranks second in driving distance on tour, and Daly is fifth. They hit every fairway except No. 9 at Tiburon's average par-72 layout, which measures 7,288 yards.
'For us, if one of us hits a decent drive, it's going to be out there far enough,' said Daly. 'We had five eagle putts today, so this is a great format for me and J.B.'
Leonard and Verplank also collected low scores by hitting fairways. After that, Leonard did it with his iron shots and Verplank made a lot of putts.
'We team up very well together,' Verplank said. 'We were very comfortable playing with each other.'
'A lot of times it just came down to picking out who's going to hit the second shot as to who's got the better number for a full shot,' said Leonard, 'and it's a pretty nice luxury to have.'
Rod Pampling and Jerry Kelly are in third place following an 8-under 64. They had eight birdies and a 32 on the front and back nine.
'I think we knocked a lot of shots really close, which certainly made it easy to get some birdies going out there,' said Pampling. 'It was just a nice, enjoyable day out there.'
Trevor Immelman and Rory Sabbatini, Brad Faxon and J.J. Henry, and Mark O'Meara and Jeff Sluman share fourth place at 6-under 66.
Chad Campbell and Nick Price are seventh at 5-under 67, one shot ahead of two teams: defending champions John Huston and Kenny Perry, and Fred Funk and Scott Hoch.
Mark Calcavecchia and Steve Elkington had a 70 and are 10th. Fred Couples and women's world No. 1 Annika Sorenstam, who shunned the LPGA Tournament of Champions this week, are one shot further back at 71.
Sorenstam, three years after becoming the first woman in 45 years to play on the PGA TOUR, is competing in her third so-called 'challenge season' tournament.
After playing in the Skins Game three straight years, this is her first multiple-round event against the men since her high-profile attempt to make the cut at the 2003 Colonial.
Tournament host Greg Norman and 2008 European Ryder Cup captain Nick Faldo are in last place following an even-par 72.
The remainder of the tournament features a better-ball round on Saturday and a scramble on Sunday.