Huston and Maggert had an eagle, seven birdies and a bogey en route to an 8-under-par 64 in the alternate-shot format, taking a slim lead over the duos of Rocco Mediate-Lee Janzen and Mark O'Meara-John Cook.
This is the third Shootout appearance for both Huston and Maggert, who have combined for eight titles in more than 600 appearances on the PGA Tour. The two played together in the 1994 Presidents Cup, losing to Vijay Singh and Steve Elkington.
"We do our own thing and don't get in each other's way," said Huston, who highlighted the round with a 30-foot eagle putt at the par-5 sixth hole.
Mediate and Janzen -- both of whom attended Florida Southern -- had seven birdies during a bogey-free 7-under 65 at Tiburon Golf Club as they seek their first Shootout titles. Janzen was a runner-up with Hale Irwin in 1996 and Chip Beck in 1995.
"We followed our game plan -- hit it in the fairway and stay out of trouble," said Janzen, a two-time U.S. Open champion.
O'Meara, who won the inaugural tournament with Curtis Strange at Sherwood Country Club in 1989, and Cook also shot a 65, a stroke better than the teams of Elkington and Peter Jacobson; Mark Calcavecchia and Andrew Magee; and Matt Kuchar and David Gossett.
The second round is a best-ball format on Saturday, followed by a scramble on Sunday.