Brian Gay carded a 3-under 69 in the third round and is alone in fourth place at minus-9. Defending champion Ben Crane shot a 1-under 71 and is in sole possession of fifth at 8-under-par 208.
In the first and second rounds, cool temperatures and winds made scoring very difficult. On Saturday, it was warmer and the wind was down. That may only last one day as the forecast on Sunday calls for wind gusts up to 30 miles per hour.
Johnson, the overnight leader and Nationwide Tour Player of the Year in 2003, lost his advantage after a bogey at the fourth on Saturday. Crane tied him atop the leaderboard, but fell one back with a bogey at the fifth. Johnson sank a 5-footer for birdie at the same hole, one group behind Crane, to go ahead by two.
Crane fell behind for good at the ninth when his approach sailed over the green. He made double bogey and never got close to the lead again.
Johnson had a comfortable margin and played like it with some looses drives. He hit his tee ball into some hay on the left side at 10, a bunker at the par-3 11th and into sand with a 3-wood past the fairway at 12. But the 28-year-old was able to save par at all three holes and keep his seat atop the leaderboard.
Johnson used the solid par saves to pick up his game. At 13, Johnson found yet another bunker, but knocked his approach to two feet to set up birdie and go three ahead of the field.
He made routine pars at 14 and 15 and even found the short grass off the tee.
While Johnson was playing solid golf on the back side, Harrington was charging. The Irishman tallied four birdies on the back nine, then birdied the 18th after attempting to go for the green in two.
Johnson's margin was now one, but the 36-hole leader hit his tee ball to three feet to set up birdie at the par-3 16th. Johnson knocked his approach 10 feet short of the hole at the 17th and rolled home the birdie putt to go three up on Harrington and Hend, who made a spectacular eagle at 18 to join the Irishman at minus-10.
Johnson had only the par-5 closing hole at the TPC at Sugarloaf. His drive landed in a drain and after his drop, he nailed his fairway metal right into the gallery. His ball was on a blanket and after two failed drops, Johnson placed his ball with no penalty on the hill where it landed.
He faced an extremely difficult shot with the slope of the green going against him and toward the water. Johnson had to hit a delicate pitch over a bunker and that's exactly what he did, landing on the fringe and watching as the ball rolled 20 feet left of the hole.
'The big pond behind crossed my mind,' admitted Johnson, who is the only player in the field to post three rounds in the 60s. 'The plan there was if I couldn't keep it on the green, then get it in the bunker. I just tried to land it over the bunker. If I did, it wouldn't release too far. I was playing the percentages.'
Johnson missed the birdie putt, but tapped in for a great par save.
Now Johnson has the 54-hole lead for the first time on the PGA Tour with win No. 1 in his radar.
'I'm going to go about it as I did today and the previous days,' said Johnson. 'I don't like to look at numbers. I go about it as my business. Two years ago, I played with Padraig on Sunday. Should be fun to play with him again.'
Harrington flew out of the gate on Saturday with two birdies in his first three holes, but lost it all with a triple-bogey 7 at the fifth. He made one more birdie on the front nine, but vaulted up the leaderboard with his play on the second nine.
The Irishman recorded four birdies in his first seven holes, including two in a row from the 10th. He had a look at birdie from 10 feet at the 17th, but the putt died on him at the hole. Harrington, who was the runner-up to Adam Scott last week at the Players Championship, made the birdie at 18 to polish off his round of 5-under 67.
Now Harrington, a week away from the Masters, has a shot at his first PGA Tour title.
'It's quite important,' said Harrington, referring to a win on the PGA Tour. 'Certainly a win on the U.S. tour is an important milestone. I'm not putting myself under any pressure that it has to happen tomorrow, but yes, a win would be very nice.'
Hend, an Australian who had not made a cut on tour until this week, was 2 under on his round until the 18th. He knocked his second shot to 5 feet and drained the eagle putt to finish his round of 68.
'I'm just trying to be composed and keep doing what I've been doing,' said Hend. 'I'm not really worried about what the lead is and what the tournament is doing, I just want to achieve my own goals this week. I'll be happy if I can achieve them.'
Mark Hensby (66), Peter Lonard (69) and Craig Bowden (72) share sixth place at 7-under-par 209. Two-time U.S. Open champion Lee Janzen and Glen Hnatiuk each posted rounds of 4-under 68 and are knotted in ninth at 6-under-par 210.
Phil Mickelson shot a 1-under 71 and is tied for 18th at minus-4.