Out early in the 10th group of the day, the American posted a second consecutive 67 to get to 8-under for the tournament and a four shot lead from the comfort of the clubhouse.
As the day wore on it looked as though no-one was going to get close to the two-time tour winner when suddenly Matsuyama, Jason Day and Louis Oosthuizen found something.
Matsuyama, 1-under and three back to start the day after a roller coaster 70 Thursday, cruised to the turn in 2-under to get in the mix then staked his claim with three straight birdies from the 12th.
That got him to 6-under, just two back and with all the momentum as he stood over his 210 metre second to the par-5 15th, seemingly ready to strike. And then the horn blew.
The stoppage could hardly have come at a worse time, Day, too, in the midst of a hot streak when dangerous weather halted proceedings.
The 2015 champion had just posted a run of eagle-birdie-birdie-birdie from the 7th to the 10th to climb to outright third just three behind Kisner.
It would be one hour and 43 minutes before players returned to the course, one that in no way resembled the Quail Hollow layout they had left a little less than two hours earlier.
Greens softened by rain were no longer borderline unplayable, instead several golf balls seen backing up after hitting the surface.
The uncertain conditions seemed to have killed the momentum of Matsuyama, Day and Oosthuizen as all produced poor first shots back. All, though, recovered quickly.
After flaring his approach to the 15th way right, Maytsuyama hit a sublime pitch to kick in range then made an extraordinary par from the hospitality tents on 16.
He followed up that act by stealing a shot on the field with an exquisite birdie on 17, the unlikely two vaulting him to a share of the lead.
A narrowly missed birdie putt at the final hole saw him sign for a course record 64, an extraordinary score on the heels of his brilliant 61 to win last week's WGC Bridgestone event in Ohio.
Day, meanwhile, hooked his first shot back, ran his second through the green and couldn’t get up and down as he made a second bogey of the day to drop back to minus four.
The mis-step looked to have killed his momentum but he hit back with a birdie from almost 50 feet at the par-3 13th to get back within three then, with the light fading fast, he backed up with another at 14.
He lipped out for birdie at 15, made a good par at 16 and with darkness falling made a par at the 17th as playing partner Dustin Johnson ran ahead to the final hole and teed off, ensuring the whole group could avoid returning in the morning.
In the end a par at the last saw the Australian finish the day two behind and outright third though that may chamnge with some players still to complete their second rounds.
Oosthuizen and Francesco Molinari share fourth in the clubhouse after Molinari matched Matsuyama’s course record 64 while last week’s PGA Tour winner, Chris Stroud, is also at 5-under and three back but is one of more than 20 players who will return to the course at 7.30am.
Of the other pre-tournament favourites it was another frustrating round for Rory McIlroy who is 10 off the pace at 2-over after a second consecutive 72.
Rickie Fowler is nicely placed at 3-under with 36 holes remaining thanks to adding a 70 to his opening 69 though as the weekend unfolds, his triple bogey Thursday at the 5th hole seems likely to come back and haunt him.
US Open champion Brooks Koepka is at 1-under and T11 while fellow bomber Dustin Johnson is 2-over after a second round 74 to be T31.
Jordan Spieth’s bid for a career Grand Slam looks like it will have to wait another year as he battled to a second round 73 and is 11 shots off the pace and sharing 46th place.
Overnight co-leader Thorbjorn Olesen unravelled after hitting his tee shot out of bounds on the par-5 15th and making double bogey then adding another at 16.
He was 6-over for his round with three holes to play when darkness stopped proceedings.