The German, who began this tournament with back-to-back 65s to reach 10 under, suffered a setback at Pinehurst when he bogeyed his second hole on Saturday.
However, playing partner Brendon Todd also dropped a shot at the same hole, meaning Kaymer, who is gunning for a second major title after lifting the US PGA Championship in 2010, remained half a dozen clear at the top of the leaderboard.
On a day when low scoring looked set to prove extremely difficult, Todd was joined on three under by Brandt Snedeker and Brendon De Jonge, the latter picking up an early birdie at the fourth.
Rickie Fowler recorded two early birdies to reach two under, the same mark as Henrik Stenson and Kevin Na, but a bogey at nine stunted the former’s progress.
Further down the leaderboard, two-time major winner Rory McIlroy made a poor start with dropped shots at the second, fourth, fifth and sixth holes and was three over for the tournament, while defending champion Justin Rose was also struggling, some 11 shots adrift of Kaymer.
However, their struggles were nothing compared to those experienced by Toru Taniguchi.
The Japanese carded a woeful 18-over-par 88 and now sits at 23 over for the tournament.
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