Needing a top three finish at Jumeirah Golf Estates to have any chance of grabbing The Race to Dubai crown away from the German, McDowell is down in joint 25th spot after a level par 72.
That was five strokes more than Kaymer, who lies third two shots behind Swede Karlsson as he kept alive the possibility of not only winning The Race to Dubai, but also earning a staggering €2,000,000 on Sunday - and taking the World Number One spot off Lee Westwood.
Karlsson was Europe's Number One two years ago, but then suffered a retina problem and after taking a three-month break did not even make the 60-strong field for this season-ending event.
This is his debut in it therefore and he very nearly kicked off by breaking Westwood's course record.
After an eagle at the long 14th, where he sank a 114 yard pitch, and birdies at the 16th and 17th he stood eight under and needed a four on the 620 yard last for a 63.
Instead he drove poorly up against a tree, ran up a bogey six and so saw his lead over Korean teenager Noh Seung-yul shrink to one.
"I'm playing pretty well," said Karlsson. "I have most of the shots in the bag. I feel pretty comfortable with where I am in the game and there's no blindness at the moment or any other diseases - so things are good!
"I just try to go out and play my best golf four days in a row and we'll see where I end up. If I think about numbers and things like that, then it's usually not very good for my game, so I just try to leave as much behind as I can, and playing one shot at a time.
"Obviously it's a low scoring course, so you need to keep it going, very important."
The two European Number One contenders were playing partners, but Kaymer reckons they exchanged "maybe two or three sentences" during the four hours they spent together.
And one of them was a simple "Well done" from the Northern Irishman after Kaymer had followed a birdie on the long second with an eagle two at the 452 yard next.
The US PGA Championship winner sank a 192 yard seven iron for that and stated: "I think the last time I holed out from the fairway was on The Challenge Tour.
"I never got that lucky, but it's the right week - the most important of my career so far - to get lucky."
McDowell, the reigning US Open Championship holder, had already noticed a "definite stand-off" between the pair when they were pictured together with their Major trophies on Tuesday, but Kaymer did add about the lack of chat: "It just happened.
"We get along well, don't get me wrong. But I just wanted to focus on my game and he wanted to do the same."
McDowell, who has been suffering from a head cold all week, will tee off nearly 2 1/2 hours earlier in the second round and is nowhere near throwing in the towel yet.
"It frustrated me a little bit playing with him because he was playing so well," he said.
"He kind of left me in the dust literally out there, so it's great to get away from him and the distraction tomorrow.
"In the morning there will be a little less grain on the greens and they will be a little less scuffed up. It should be a good chance to make some putts.
"He's a pretty emotionless guy and would be a helluva poker player. He's a cool customer - there were no signs of any nerves and I was very impressed."
Asked about his own health he commented: "No room for excuses. I have to come out and feel 100 per cent and ready to go.
"I'm here to do a job and I certainly haven't shot myself in the foot just yet. He's five ahead of me, that's all."
Kaymer insists he does not have room in his head to think about the World Number One situation.
A top two finish, but more likely a win, could take him ahead of Westwood, whose defence of the tournament started with a three under 69 for a share of fifth place.
Westwood is still suffering from the calf muscle injury that has bothered him most of the year.
"Everybody's got to remember I'm still rehabbing," he said. "I've not been able to work on my game and it does not help that it's as hot as it is - it makes it swell.
"I'm hoping it'll be back to 100 per cent next season and I'm looking forward to not having to worry about it. I showed I was rusty and was not competitive sharp, but I hit only two iffy shots all day.
"I've played once in the last five weeks (he was runner-up in Shanghai at the start of this month) and was 18 under.
"That's pretty good going and I'm pleasantly surprised how I'm playing."