SHANGHAI, November 1, 2013 (AFP) - Completing a sizzling front nine of 30, Johnson took just 33 more to get home to lead on 12-under par 132.
Overnight leader McIlroy of Northern Ireland was five shots back tied for second after a level-par round that had promised much more.
The 24-year-old had threatened to repeat the heroics of his first day 65 when he had a hat-trick of birdies on the sixth, seventh and eighth.
But a bogey at 11 caused the self-doubts to creep back in and he dropped two more for a 72.
"Just one of those things," he told reporters after, clearly frustrated. "I hit a couple of bad shots... and I started to doubt myself sometimes. Didn't hit a lot of quality shots on the back nine."
McIlroy was joined at seven under by two Americans, Boo Weekley (67) and Bubba Watson (69) as the Stars and Stripes started to climb the leaderboard dominated by European players on day one.
"I'm definitely happy with where I'm at," said world number 23 Johnson afterwards, whose 63 tied the course record jointly held by McIlroy, Daisuke Maruyama, Ernie Els (all in 2009) and Martin Kaymer (2011).
"I drove the ball really, really well for two days and for me that's a big key," added Johnson. "I hit a lot of good iron shots and though it's tough to get close to these holes I made a lot of nice 10- to 15-footers."
Watson, who won the Masters in 2012, told AFP earlier this week that he thought the course and greens would suit him on his first visit to Sheshan Golf Club. He was as good as his word, shooting a second-round 69 to add to his 68 the previous day.
He said he was surprised at how similar it was to playing back home on his first visit to China. "You don't hear a lot of English," he joked. "But it's about the same.
"Everything about the trip has been beautiful. Malaysia last week (CIMB Classic) and then here. It's perfect."
Weekley had one of the rounds of the day with a five-under 67 to tack on to his opening 70.
Unfortunately his post-round interview was more staccato than his golf and a little undiplomatic to his hosts.
Asked how he liked being in China, Weekley replied: "It don't matter. We're here."
And had he seen anything of China apart from the hotel and the golf course? "You said it exactly, hotel, golf course. I'm all right. I don't need to see nothing."
Former US Open champions Graeme McDowell of Northern Ireland is second in the Race to Dubai European Tour standings with this and just two more events remaining.
He is intent on closing the gap to leader Henrik Stenson and has shown a welcome return to form after what he described as a "rusty" performance at last week's BMW Masters in Shanghai after taking five weeks off to get married.
His second successive 69 Friday, playing alongside Johnson, took him to a share of fifth place on six under par.
"Yesterday was very solid. Today was a little untidier," he said after his round.
"It was kind of tough to focus with Dustin Johnson hitting it 350 yards down the middle of every fairway. But I was happy that I hung in there. Happy to shoot three-under."
Stenson has had a miserable week so far. The Swede, who won the FedEx Cup in September, shot a four-over 76 and is six-over par for the tournament, languishing in 70th place in the 78-man field.
He needs a big improvement over the weekend as nearest rivals McDowell, Justin Rose (five-under after two rounds) and last week's big money winner Gonzalo Fernandez-Castano (six-under) are all in contention for the $1.4 million winner's cheque heading into the weekend.
Leading scores on Friday after the second round of the $8.5 million World Golf Championships-HSBC Champions at Sheshan Golf Club, Shanghai (par 72):
132 - Dustin Johnson (USA) 69-63
137 - Bubba Watson (USA) 68-69, Boo Weekley (USA) 70-67, Rory McIlroy 65-72
138 - Tommy Fleetwood (ENG) 68-70, Sergio Garcia 70-68, Gonzalo Fernandez-Castano (ESP) 67-71, Ernie Els (RSA) 69-69, Graeme McDowell 69-69, Ian Poulter 71-67
139 - Jeong Jin (KOR) 70-69, Liang Wenchong (CHN) 72-67, Phil Mickelson (USA) 71-68, Justin Rose (ENG) 68-71, Keegan Bradley (USA) 71-68, Graham DeLaet (CAN) 71-68, Jordan Spieth (USA) 68-71
140 - Billy Horschel (USA) 71-69, Louis Oosthuizen (RSA) 70-70, Jason Dufner (USA) 73-67, Gaganjeet Bhullar (IND) 69-71, Mark Brown (NZL) 72-68
141 - Luke Donald 70-71, Mikko Ilonen (FIN) 72-69, Francesco Molinari (ITA) 72-69, Jamie Donaldson (WAL) 67-74