Kisner set the pace by posting a 4-under-par 67 for the second day in a row before Matsuyama notched a bogey-free 64 later in the day.
They both sit at 8-under 134 for a two-shot lead on the rest of the field, though several players will have to complete rounds Saturday morning after play was suspended due to darkness.
Matsuyama played during the rain-interrupted afternoon round.
Australian Jason Day is in the third place at 6-under with two holes to complete in the round.
Italian Francesco Molinari finished at 5-under through two rounds after his 64, while South African Louis Oosthuizen is also at 5-under after his 67.
Matsuyama made a big jump in the afternoon. He tied Kisner with birdie on the 17th hole. Earlier, Matsuyama strung together four consecutive birdies, with the last one coming on No. 15 after play resumed.
Kisner continued what had been a late surge Thursday by posting birdies on two of the first three holes in the second round, which he began on the backside. Then on No. 7, he posted an eagle for the only hole he didn't post a par on that side.
Day, the 2016 runner-up, surged with a 5-under mark so far in the round. He had an eagle on No. 7 followed by two birdies and completed 10 holes before the delay.
Jordan Spieth, in his first quest to complete a career grand slam, is at 2-over for the tournament with one hole to play in the second round.
Rickie Fowler stayed in contention with a 70, moving to 3-under for the tournament.
D.A. Points appeared to be Kisner's biggest threat until double-bogeys on Nos. 16 and 17 pushed him to 1-under for the tournament. Points ended up with 73 in the round.
Play was halted at 4:43 p.m. because of dangerous weather looming. The suspension lasted about 1 hour, 45 minutes.
First-round co-leader Thorbjorn Olesen of Denmark was 6-over through 15 holes of the second round, falling all the way to a 31st-place tie.
Phil Mickelson, who followed Thursday's 79 with a 74, will miss the cut in the PGA Championship for the first time in 22 years. Mickelson didn't have a birdie until his 31st hole of the tournament. His 79 was his worst round in a PGA Championship.
NOTES: Steve Stricker will make the cut in a major for the 26th consecutive time, going to the weekend at 3-over following his second-round 70. ... Defending champion Jimmy Walker had 69 after a first-round 81, missing the cut at 8-over. ... Though Omar Uresti is a former PGA Tour player, he never qualified for this tournament until making it as a club pro this year. He advanced to the weekend at 2-over through two rounds. ... Si Woo Kim withdrew from the tournament citing a back injury. He shot 79 in the first round.