Weir established a new 54-hole record at this event with his 17-under-par-196 total. Fred Couples held the previous mark at 197 in 1990 and Couples went on to the winner's circle that year.
Maruyama birdied the last to post an even-par 71. Jeff Maggert shot a 2-under 69 to take third place at 11-under-par 202, followed by Scott McCarron, who carded a 1-over 72 on Saturday for a solo fourth at minus-10.
John Daly will have to make up a lot of ground if he is to win two weeks in a row on tour. Last week's Buick Invitational winner put up a round of 1-over 72 and is tied for fifth place with Mercedes Championships winner Stuart Appleby (70), Loren Roberts (69) and Briny Baird (73). That group is at 9-under-par 204.
Tiger Woods never mounted a charge on Saturday. He struggled to a 1-over 72 and is tied for 44th place at 3-under-par 210.
Saturday's round featured cooler temperatures and steady rainfall. As the round pressed on, the rain intensified but all 78 players completed their third rounds, albeit on a much longer course than earlier in the week.
With the increased length the rain brought, the storyline of the third round was the difference in play by the leaders on Riviera Country Club's final three par-3 holes.
The second-round leaders remained knotted until the par-3 sixth. Weir sank a 16-foot birdie putt to go to 13-under par, while Maruyama made bogey and fell two behind.
'That got momentum on my side,' Weir said.
The margin held at two as both players tapped in short birdie putts at the 10th and each made lengthier birdie tries at No. 11. The next swing hole came at another par-three, the 14th.
Weir landed his tee ball 17 feet long and left of the hole while Maruyama pushed his iron shot right into a greenside bunker. Maruyama blasted out to 20 feet and missed his par putt but Weir cashed in his birdie opportunity to complete another two-shot swing and move four ahead of Maruyama, his closest competitor.
At the 166-yard 16th, Weir hit his first to 11 feet but Maruyama missed the green left of a bunker. He pitched to 12 feet and his par-saving putt died short of the hole. The reigning owner of the green jacket poured his putt in the center of the cup and now it was a six-shot advantage.
'It was a tough day out there. I really leaned pretty hard on my short game today,' said Weir.
Although Weir seems to have a commanding lead, history has not been kind to the Canadian left-hander when he owns at least a share of the 54-hole lead. Weir has had a piece of the 54-hole lead five times in his PGA Tour career and has posted zero victories with his best finish a second at Doral in 2001.
'I'm looking at this as a big challenge,' said Weir, whose six tour victories have all been comebacks. 'I want to prove to myself that I can handle leading by five shots like I am. I want to go out there and play solid golf tomorrow and make whoever is challenging tomorrow do something phenomenal to catch me.'
Maruyama birdied the final hole to close within five of Weir's lead at 12- under-par 201.
Tim Clark (64), Carl Pettersson (68), J.J. Henry (65), Hank Kuehne (68), Aaron Baddeley (69) and Kirk Triplett (72) share ninth place nine shots out of the lead at minus-8.