Couples and Scott stand at 19-under-par 125 through two rounds at Tiburon Golf Course. They hold a two-shot lead over John Houston and Kenny Perry, who played their final two holes at minus-3 to finish with a 63 and make the final pairing.
Mark O'Meara and Nick Price are in fourth place at 15-under after a 65, while Ryan Moore and Jesper Parnevik also shot a 65 to finish the round one stroke further back in fifth.
In the better-ball format, each golfer plays through every hole using his own ball. The player whose score is the lowest counts as the team score for that hole.
Like first-round leaders Funk and Gore -- as well as two-time defending champions Hank Kuehne and Jeff Sluman -- Couples and Scott possess a balance of distance and accuracy which is so important in an event like this.
'We talked about playing together a long time ago, and obviously I love the way he hits the ball,' Couples said of Scott, who is 21st in scoring average and 23rd in driving distance on the PGA Tour this year.
'As you saw today, he (Scott) drives it a hundred miles. He's got a beautiful stroke, and you're never in trouble.'
Impressively, the leaders strung together six birdies in a row to reach 15 under after 10 holes.
During that stretch, Couples rolled in a 3-foot putt after just missing a hole-in-one at the par-3eighth. He also sunk a 5-foot birdie putt at 10 to get to minus-15.
Couples and Scott both missed long putts at the par-4 11th to end their birdie streak, but they still held a three-stroke lead over Huston and Perry.
At the 12th, Couples lipped out a very long uphill putt that would have moved the duo four clear. Instead, they were ahead by two shots after Huston and Perry reached 13 under.
But Couples and Scott restored their three-stroke lead with a birdie at 14, and then extended it to four shots when Scott chipped in for birdie from the fringe at the 15th to put them at minus-17.
Couples made par from the fringe at the par-3 16th, and the overnight lead was pretty much in hand for the duo at that point. For Scott, it was a matter of following his partner's lead.
'I figure I'll just saddle up again and ride him like I did today,' Scott said, looking forward to Sunday's scramble and eyeing the $630,000 winner's share of the $2.6 million purse.
Of course, their lead looked a lot stronger before Perry finished with eagle-birdie on his and Houston's final two holes.
'It's a bit of a shootout, I guess,' said Scott.
Kirk Triplett and Jay Haas are alone in sixth place at 12-under-par 132 after a second-round 65.
Sluman and Kuehne (67) have some ground to make up if they are going to three- peat. They share seventh place at minus-11 with the teams of John Daly and Tim Herron (65) and Mark Calcavecchia and Loren Roberts (63).
Paul Azinger and Olin Browne shot a 68 and are in 10th place at 10 under, while tournament host Greg Norman and partner Steve Elkington are one stroke further back in 11th after a 66.
Peter Jacobsen and Scott McCarron (69) are last at minus-7.