Robert Gamez (65), Briny Baird (67) and Chris DiMarco (69) are tied for third place at 10-under-par 200.
Retief Goosen shared the second-round lead with Baddeley but opened with a triple-bogey at No. 1. He carded a 2-over 72 and is tied for eighth place at 8-under par.
Baddeley did all of his damage on the front side at Waialae, as conditions were much more difficult on Saturday thanks to winds that reached 25 mph, firming up many of the greens.
The young Australian birdied No. 2 and holed a 12-footer for birdie at the fourth. At the par-3 seventh, Baddeley rolled home a 25-foot birdie putt to reach 13-under par and go two clear of the field.
At the 510-yard, par-5 ninth, Baddeley had only an 8-iron in his hands but thanks to a drive that landed in the right rough, his ball bounded 40 feet from the hole. Baddeley sank the long eagle putt to complete a front-nine, 5-under 30 and put him five shots ahead.
'I played very well on the front nine,' said Baddeley, who earned his PGA Tour card by finishing 10th on the Nationwide Tour money list in 2002. 'I hit it close a few times. I was quite relaxed the whole time. The tee shot on one calmed me down.'
Baddeley missed several greens on the back nine Saturday but a solid short game, coupled with only 24 putts for the round, kept him in the top spot.
At the 16th, Baddeley drove into the left rough behind trees. He smoked a low shot that flew through the green and into a back bunker, leaving him with a down-wind, downhill blast out of the trap. Baddeley's shot out of the sand left him with six feet and the 21-year-old calmly drained the putt to save par.
Baddeley had no real chance at birdie on the last two holes as he had 30 feet for birdie at 17 and drove in the rough at 18. But the young Australian has the 54-hole lead in his first event as a member of the PGA Tour.
'I thought I played alright on the back side, I just missed a couple of greens,' said Baddeley. 'The swing still felt good out there. I only just missed the greens. I'm looking forward to tomorrow.'
Sunday's final pairing will feature Baddeley and Els. In the last week, Els established a new PGA Tour record for scoring in relation to par with his 31-under, eight-shot drubbing of the field at the Mercedes Championships, which moved him to second in the World Golf Rankings.
Baddeley is a battle-tested rookie in the golf world. He won two Australian Opens before he turned 20 and bested Sergio Garcia in a playoff to capture the 2001 Holden International.
'I'll go out and I'm just going to enjoy it,' said Baddeley. 'Ernie's a laid back fellow. I get along well with Ernie. I think tomorrow is going to be a good day. All I can do is get out there and golf my golf ball and if I can do that, hopefully I can get a win.'
Els got into second place with a birdie at the 14th but he still trailed Baddeley by four. He holed a 12-foot birdie putt at the 16th and made it two in a row with a 20-footer at the 17th to get within striking distance of Baddeley.
'You just have to try and keep going,' said Els, who shot a 4-under 66 on Saturday. 'The greens were so fast today. You have to hit a lot of greens and then try and get your putter hot.'
Els knows that despite his huge success of late, he will have to do more than just show up to visit the winner's circle on Sunday.
'He's obviously very hungry to win his first event,' said Els, who can become the first player since Steve Jones in 1989 to win the first two events on a PGA Tour calendar. 'He's got a lot of talent. He's very much going to be a star of the future. Obviously, he's a guy for big occasions. He's definitely not scared. This is the big leagues, now, but he's a big-league player.'
Shigeki Maruyama is alone in sixth place at 9-under par, followed by Goosen and Robert Allenby, who are tied for seventh at minus-8.
Jerry Kelly, the 2002 Sony Open winner, is part of a group in ninth at 7-under-par 203. Among the other players who are tied for ninth place are 1995 U.S. Open champion Corey Pavin, Fred Funk and 1999 Sony Open champion Jeff Sluman.