Despite earlier dropping two shots at the 10th, Johnson reached the 18th with his five-shot halfway lead intact thanks to a front nine of 30 for the second day running and four birdies in a row from the 13th.
But the American drove into the water down the right of the par-5 18th and found a bunker with his fourth shot, eventually signing for a seven and a third-round 66 to lie 18 under par.
Defending champion Ian Poulter is Johnson's nearest challenger after a superb 63, with Ryder Cup team-mate Graeme McDowell a shot further back after a 64.
US Open champion Justin Rose, first-round leader Rory McIlroy and Canada's Graham DeLaet are all six off the pace on 12 under, Rose and DeLaet shooting 65 and McIlroy returning a 67. Germany's Martin Kaymer is 10 under after setting a course record with a flawless 62.
"I'm still a little mad from my double bogey on 18," Johnson said. "Obviously to have a three-shot lead going into the last day is good and I am looking forward to the challenge"
Poulter, looking to become only the second man after Tiger Woods to successfully defend a WGC title, charged up the leaderboard with five birdies in a row from the third and another on the ninth to be out in 30. When he holed from 20 feet for an eagle on the 14th the gap was down to one, but Johnson responded with birdies on the 13th, 14th, 15th and 16th.
Poulter three-putted the 17th for his only bogey of the day but birdied the last to stay firmly in the hunt for the top prize of £856,000.
McDowell will not have given up the chase, the Northern Irishman winning the 2010 US Open after Johnson squandered a three-shot lead in the last round.
Meanwhile, Scot Andrew McArthur launched himself into contention for European Tour graduation and the title at the Dubai Festival City Challenge Tour Grand Final thanks to a four-under-par third round of 68, leaving him five off the lead, held by Shiv Kapur, in tied third.
The Glaswegian needs a high finish to make an 11th-hour climb into the Challenge Tour Rankings top 15 and win a place in the 2014 Race to Dubai.
He said: "It will be very exciting tomorrow. I know what I need to do so I just have to see if I can do it. There will obviously be a bit of pressure but I need to focus on the shots and not the situation."