After opening with a 63, Frost had a 13-under 129 total. The South African made an 18-foot putt for the eagle on the par-5 18th, while Couples two-putted from 35 feet for birdie and a 66 of his own.
"It was a day where Freddy and I battled it out," Frost said. "We were on top of the leaderboard all day and he made a nice birdie on 10 and I followed it with one and we did the same thing on 13. I think we played steady golf."
Jim Gallagher Jr. was third at 8 under after a 68, and Scott Hoch (64), Jay Haas (66), Bob Tway (67) and D.A. Weibring (68) were another stroke back at Newport Beach Country Club. Hoch is making his second start after returning from left hand and wrist injuries.
"You never know, someone could go out and shoot 63 early in the day that can always happen," Frost said. "I just will have to play my normal game and 68 will be a good score. I'd take that right now."
Couples spent more time on the range before the round to stay loose, but battled his driver most of the day. He hit only six of 14 fairways, but was more frustrated with his short irons.
"I let a couple of easy 8-iron shots go," Couples said. "I bogeyed the fourth hole and the sixth hole from 145 yards, which really kind of killed me, but I made it up with a few good putts. ... He's one ahead and I'm not going to be able to shoot a 68 or 69 and win. I have to shoot something very, very good."
Couples, the event winner in 2010, had 26 putts after needing 28 the first day.
"For some reason a lot of people struggle on these greens and I do struggle at times, but very rarely with the speed of the greens," Couples said. "That certainly helped me today with 30-40 footers getting them up there close."