Peter Lonard (67), Matt Gogel (68) and K.J. Choi (68) share third place at 11-under-par 205.
Maruyama opened Saturday's third round with a five-shot lead and maintained that advantage through the first six holes as he and Faxon traded a pair of birdies each.
Things turned at the par-4 seventh. Maruyama missed the green with a pitching-wedge then took a few chips before he reached the putting surface. He left the hole with a double bogey and Faxon made par so the lead was down to three.
'I hit it farther than expected, and the place where the ball was, it was the toughest place to reach the hole,' said Maruyama. 'And the grass is bermuda grass. It's one of my unfavorite grasses, so it was really tough to approach the ball to the hole.'
Faxon capitalized on Maruyama's miscue. Faxon sank a six-foot birdie putt at the ninth while Maruyama missed a 12-footer for birdie of his own. Faxon was now two shots behind but cut into that lead when he ran home a 30-footer for birdie at the 11th.
At the par-5 13th, Faxon drove left and his ball stopped against a tree. After he took a penalty drop, Faxon knocked his third down the fairway. He pitched his fourth to six feet. Maruyama drove through the fairway but hit his second to eight feet. Maruyama canned his eagle putt and Faxon made his par so Maruyama went ahead by three once again.
'That was the perfect hole,' said Maruyama. 'A perfect shot from the tee box, a perfect 3-iron, the second shot, and perfect putt. That hole saved my game today.'
Maruyama had some opportunities late in his round to extend the lead but did not take advantage. At the par-5 15th, his ball landed on the green in two but the ball caught a ridge and rolled back down into the fairway. His third stopped eight feet from the stick but Maruyama could not find the bottom of the cup.
He made a couple of testy par saves on the final few holes, including a 24-footer at 18, to take the 54-hole lead in a PGA Tour event for only the second time. The other tournament was last year's Byron Nelson Classic, his most recent win on tour.
'Of course I'll feel the pressure tomorrow, but also Brad Faxon should feel the pressure to catch up with me tomorrow, so it's even,' said Maruyama.
Faxon, who lost a playoff to Bob Tway this year at the Canadian Open, holed a 45-footer for birdie at the fourth, then made it two in a row with an eight-foot putt at No. 5.
Faxon, one of the top putters in history, missed chances at seven when his 15- foot birdie try lipped out and at the eighth, his six-footer for birdie missed as well.
The Boston Red Sox fan finished with a 4-under 68 and has a chance at his first win since the 2001 Sony Open in Hawaii.
'It would mean a lot to me,' admitted Faxon. 'A big goal of mine going into this year was to win a tournament, and there's not many left. I feel good where I've been the last month with my game.
'Certainly Shigeki is playing well, and he made a great finish with his eagle on 13 and nice par putt on 18. I enjoy playing with him. I'm looking forward to tomorrow.'
Robert Allenby (66), Steven Alker (68), David Sutherland (69), Stephen Ames (71) and last week's Las Vegas Invitational winner Stuart Appleby (68) share sixth place at minus-10.