Karlsson, one of the four Europeans warming up for next weeks Ryder Cup, was penalized for grounding his putter when his ball moved slightly on the second green.
I was over the ball but hadnt addressed the club right behind the ball, said Karlsson, who hasnt won since 2006. The ball moved forward and I thought there wouldnt be a penalty because I hadnt addressed it, but its actually enough that the putter is on the ground.
He finished at 12-under 204 for a three-shot lead over Francesco Molinari of Italy and Jean-Francois Lucquin of France, who won the Omega European Masters in Switzerland last Sunday. Molinaris 65 was the best round of the week.
Karlsson qualified for his second Ryder Cup with nine top-10 finishes this season.
His Ryder Cup teammates, Miguel Angel Jimenez and defending champion Soren Hansen, shared 12th place after shooting 68 and 73, respectively, while Northern Irelands Graeme McDowell was 23rd after a 70.
Ive played this course in 12 under with a penalty shot, thats the most important thing, Karlsson said. Tomorrow I just have to keep going. It would be great to have a seven-shot lead, but I would have been happy with a one-shot lead also.
Molinari made an eagle and three birdies in the space of five holes on the back nine.
It was a really good day. It was one of those days where almost everything goes in and hopefully I can do something like this tomorrow as well, he said.