The 25-year-old German looked set to trail overnight leader Alejandro Canizares before the Spaniard collapsed with two late double bogeys.
A level-par 71 for a nine-under 204 aggregate left Kaymer a stroke in front of Canizares (73) and Briton Steve Webster (70).
Canizares, son of former Ryder Cup player Jose Maria, held a three-shot lead going to the 16th but found a hazard at the par-three hole and then hit his approach into a lake at the 18th.
“It was tough to see Alejandro finish like that,” playing partner Kaymer told reporters. “You want to lead but you don’t want to see that.
“I didn’t play well but I kept it together. To win twice here would be awesome.”
Kaymer, who was reprimanded for wearing a Germany soccer shirt in last week’s BMW International final round in Munich, was delighted to hear his country had beaten Argentina 4-0 in the World Cup quarterfinals in South Africa.
“I was one over par after a few holes when my caddie told me we were winning 1-0, then when I made a birdie on nine I heard it was 2-0. It kept me hanging in there, I’m sure,” he said.
A thunderstorm delayed the start for more than four hours before Canizares took early control with two birdies in the first three holes.
However, after his late mistakes the Spaniard will need to regroup if he is to claim his second title.
In Newtown Square, Pa., Justin Rose was happy to be leading the AT&T National, especially because it was only five days ago that he threw away a chance to win with a surprising meltdown in the final round.
Tiger Woods? He’s happy to still be playing.
Rose played bogey-free Friday and wound up with the best score of the tournament, a 6-under 64, to build a one-shot lead over Jason Day (68) and Charlie Wi (65) going into the weekend at demanding Aronimink Golf Club.
Woods, who won this tournament last year at Congressional, hit the ball well for the second straight day. He again got nothing out of it, however, and missed a 30-inch putt late in the round that brought him back to a 70. He was at 3-over 143, which made the cut on the number, although he was never in serious danger of going home early.
In his first tournament since winning the Memorial by closing with a 66, Rose had a three-shot lead at the Travelers Championship in Cromwell, Conn., when it all fell apart. He shot 39 on the back nine for a 75 and tied for ninth.
In Sylvania, Ohio, Na Yeon Choi followed her opening 7-under 64 with a 67 to take a two-stroke lead in the Jamie Farr Owens Corning Classic.
Choi has needed just 53 putts in 36 holes while getting to 11-under 131 at Highland Meadows Golf Club. South Korean compatriot Inbee Park (66) was tied for second with Christina Kim (67) and Canadian Alena Sharp (68).
Kristy McPherson holed a 60-degree wedge from 75 yards on the 18th hole for an eagle and a 68 to lead a pack of six players at 6 under.
