It was the third time in four years Kaymer has won the tournament and he did it by a thumping eight-shot margin over Rory McIlroy on Sunday.
With Woods overhauled, top man Lee Westwood needs to on his guard with Kaymer seemingly on the march to the world number one spot.
The German needed only a top-seven finish to take over as number two from Woods, but won at a canter from a field which included the other three current major champions, and also Westwood, who ended up 64th, out-scored by a massive 26 strokes.
The last time a pair of Europeans filled the top two positions in the world was Nick Faldo and Bernhard Langer 18 years ago - and Woods will start his season at Torrey Pines in California this week down in third spot for the first time since October 2004.
Amazingly, Kaymer did what he did not having played a tournament since clinching the European Tour money list crown in November.
The 26-year-old, five clear of McIlroy with a round to go, closed with a 66 for a tournament-record 24-under-par total of 268.
"He's killing us," said Retief Goosen after a best-of-the-week 64 brought him into a tie for third with Graeme McDowell 10 behind. "I never saw anything above 20 under round here."
Kaymer did not have a single bogey in his final 60 holes - and he has had only two in his last 97 holes on what he now jokingly calls "my home course".
He has finished first, second, first and first since missing the halfway cut on his maiden visit in 2007 - and is a cumulative 80 under par.
This was Kaymer's 100th European Tour event and his ninth success. McIlroy, albeit five years younger, has had only one in 82 starts.
The young Ulsterman, also emerging this week from a long winter break during which he suffered swine flu, will be delighted by three eagles and 18 birdies.
But he had eight bogeys compared to Kaymer's one, which came when he shanked out of a bunker into water on the 12th hole of his opening round.
Padraig Harrington, lying second when he was disqualified over a ball-marking incident on Thursday, was reduced to a commentating role as a result.
He was as impressed as anyone by Kaymer.
"He's probably the most formidable player in the world when he is leading," said the Dubliner.
"He seems to intimidate the rest of the field into believing that if he gets in front he is going to win."
Any hopes McIlroy had of applying some pressure effectively ended when he bogeyed the third and fifth.
Kaymer had already added two birdies by then and more to come on the 10th, 13th, 16th and 18th, each of them just icing on the cake as he won the trophy to keep for his hat-trick.
"It's just the perfect course for me," he said. "It was more difficult, but I hit a lot of fairways and my putting was amazing.
"It was just one of those weeks when everything goes my way.
"I never expected my career to go this fast. There was not a lot to improve this week, but there's always something and I'll be working on my game before Qatar in two weeks."
Kaymer still considers Woods the best player in the world and said of being ahead of him in the rankings: "Hopefully I can stay there for a while."
Europe also has three of the top four with US Open champion McDowell now ahead of Phil Mickelson rather than just level with him. Masters winner Mickelson managed only 37th place in what was his first event since mid-November.
McIlroy, meanwhile, moves up from 12th to seventh.