Defending champions Jeff Sluman and Hank Kuehne are in second place at 8- under-par 64. Tournament host Greg Norman and partner Scott McCarron posted a 7-under 65 and are tied for third with the long-hitting duo of John Daly and Rory Sabbatini.
Friday's action at Tiburon Golf Club was contested under modified alternate-shot format. Both players hit their drives, selected the best one, then alternate shots from there.
Leonard and Flesch combined for a birdie at the first hole, then Leonard's putter took over. He ran home a 12-foot birdie putt at the third and added a 10-footer at the next hole.
Flesch got into the act a few holes later. He drained a 10-foot birdie putt at the par-5 sixth, and collected the team's fifth birdie of the front nine at eight, after Leonard's tee ball stopped 3 feet from the hole.
On the second nine, Flesch's iron game kept the team going. He gave Leonard an 8-footer for birdie at the 10th, then Leonard, the 1997 British Open champion, sank a 30-footer for birdie at No. 12.
Leonard, who lost a playoff to Vijay Singh at the PGA Championship, knocked the squad's third to 8 feet at the par-5 14th. Flesch rolled in the birdie putt and closed with an 8-footer for birdie at 17 to take the first-round lead.
'We got off to a great start,' said Flesch. 'We both drove it in play all day, which you have to do in this format. Justin putted so great that it took the pressure off.'
Leonard was happy with the start because of the change in format on the weekend. Saturday's action is played under best-ball format and Sunday will be a scramble, both formats that induce low scores.
'It's hard to make up five or six shots with the next two formats,' said Leonard. 'You need a good start so we don't have to make up that kind of a margin.'
The defending champions flew out of the gate on Friday. They birdied the first two holes from inside 3 feet, then Kuehne converted a pair of 10-foot birdie putts at four and five. Sluman holed a 5-foot birdie putt at six and Kuehne made a 12-footer for birdie at nine to make the turn at 6-under 30.
The tandem parred their first four holes on the back nine, then birdied the par-5 14th. Sluman and Kuehne closed with back-to-back birdies at 17 and 18 to get within one of the lead.
'We played well and got off to a great start,' said Kuehne. 'It's fun having Jeff as my partner. Things really went well and we hit some quality shots today.'
Mark Calcavecchia and Loren Roberts are alone in fifth place at 6-under-par 66, followed by Scott Hoch and Kenny Perry, who teamed for a 5-under-par 67.
Paul Azinger and Olin Browne have sole possession of seventh place at 4-under-par 68, while the Haas family, Jay and his son Bill, are alone in eighth at 3-under-par 69.
Rocco Mediate replaced Peter Jacobsen Friday morning and joined Steve Elkington in a round of 2-under 70. They are tied with Fred Funk and Nick Faldo in ninth place.
Chad Campbell and Chris Riley share 11th with Charles Howell III and Lee Janzen at minus-1.