Day, the 2015 PGA Championship victor and runner-up past year, had dropped a shot on day two but a stunning tap-in eagle at the par-5 seventh hole at Quail Hollow preceded three consecutive birdies as he raced to a five-under-par total.
The threat of lightning in North Carolina meant play was disrupted for nearly two hours, but Matsuyama managed to pick up from where he left off at the 15th hole and eventually drew level with American Kisner, who managed to complete his round before the weather took a turn for the worse.
He came close to finishing with three straight birdies when his putt for a three on the par-four ninth stopped on the edge over the cup. He said at the time he had shot the stunning score despite being uncomfortable with his swing, words he repeated pre-tournament here.
The advantage of warm weather and, for the first time all week, plenty of sunshine was a slightly drier course that allowed the ball to roll.
Japan's Matsuyama, the world number three, moved to eight under despite a stoppage of nearly two hours because of potentially "dangerous" weather.
Jason Day said he was able to smash driver off the tee because his ball was less likely to bounce through the fairways and into the rough.
Now, it's a sprint to the finish.
One shot behind him were South African 2010 British Open champion Louis Oosthuizen, Italian Francesco Molinari and American Chris Stroud. "When I start hitting it the way I am now, I play well".
It appears Jordan Spieth will have to wait another year to try and win the career Grand Slam. Friday's rain has taken some of the fire out of the course, though the greens remain devilishly fast.
And while Matsuyama was in the better side of the draw, he did most of his damage before the storms arrived. He already has two World Golf Championships title and 14 victories around the world, six of them in the last 10 months.
The cut line now stands at 5 over. So, the first holes were shaky by any standard and I was three-over.
Quail Hollow, so frightening on Thursday and the early part of Friday, suddenly looked vulnerable.
He made his par putt on the 17th hole and then sprinted to the 18th tee and promptly knocked his tee shot down the middle.
The last group has five holes left to play, so Round 3 is not expected to begin until 10 a.m. or 40 minutes after the end of Round 2. And it gave new life to Scott, who will miss the next three weeks to be with his expectant wife.
It took Stroud 13 years and 290 PGA Tour starts before his breakthrough in Reno.
It's taking a while for the players to complete rounds at Quail Hollow.