Overnight leader Kisner had extended his lead after back-to-back birdies at the 13th and 14th saw him move to eight under for the tournament.
But, after struggling off the tee down the last, Kisner then found the Barry Burn and could only scramble for a six on the par four.
It left him in a tie of the clubhouse lead at six under with Zach Johnson, Pat Perez and Zander Lombard – the latter having played seven holes of his second round.
Jordan Spieth, who dropped four strokes in the final four holes to finish one over on Thursday, was surging up the leaderboard among the day’s later starters, who were playing in much drier conditions.
The defending champion made birdies at the third, fifth, 10th and 11th to sit three under for the tournament.
Tony Finau was one stroke off the leaders, alongside Tommy Fleetwood who was among the early finishers.
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