The German birdied the last two holes to complete a four-under 66 and a 10-under 200 total, one stroke better than Swede Christian Nilsson and Paraguay's Fabrizio Zanotti.
It looked as though it might prove a frustrating day for the winner at Whistling Straits last month -- until things turned Kaymer's way down the closing stretch.
Having watched three putts lip out on the back nine, his ball at last did the decent thing on the 17th hole by going in from 10 feet.
Despite a three-week break Kaymer is showing why he was not only tipped to triumph this week but is also the favorite to crown a magnificent season by winning Europe's money-list.
"My caddie told me we might not play tomorrow because bad weather is forecast," the 25-year-old Ryder Cup qualifier told reporters.
UP AND DOWN
"He asked me if we could perhaps play a little more aggressively. I definitely played aggressively on 17 and my ball went a lot further than I thought on 18 so it needed a good up and down."
A confident Kaymer said he expected to win from this position.
"The Ryder Cup was a main goal, now I have another goal -- to win the order of merit so every time I play is important," he added.
Zanotti (65) and Nilsson (68) had mixed success on the soaked, spongy greens.
Both holed long putts to get toward the top of the leaderboard before three-putting late on.
Belgian Nicolas Colsaerts, India's Shiv Kapur and Spaniard Gonzalo Fernandez-Castano were two shots behind Kaymer.
(Editing by Tony Jimenez)