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The Swede beat the World Number One by a single shot after both hit closing rounds of 67 – but that barely told the story of a rollercoaster final round at Lake Malaren.
One ahead of McIlroy overnight, the 35 year old's sixth European Tour victory looked certain when he went four clear.
However, a thrilling finish materialised when McIlroy eagled the 15th, birdied the next to narrow the gap to two and then saw Hanson find sand at the short 17th.
The World Number 25 saved par from 15 feet, but still had a scary moment when his approach to the last came down in the bank of a bunker.
After being refused relief for a plugged lie, he did well to chip to ten feet and two putts for bogey and a 21 under par total were good enough after McIlroy had just missed his 15 foot birdie attempt from the back fringe.
Luke Donald and Ian Poulter, two more of Europe's side in Chicago last month, finished third and fourth.
“It was a little bit tense,” said Hanson. “Rory made a tremendous effort with his eagle on 15 and birdie on 16, so it put quite a bit of pressure on me. I was trying to play it a little bit safe but against the World Number One you still have to hit the shots.
“I’ve been hitting it nice and especially the putter has been feeling great. Rory gave me a bit of a cushion early today – he missed a few short putts over the first few holes – and in the end that was all I needed.
“My putting has really improved, especially over the last year, and I think that’s the main reason I’m standing here with this beautiful trophy.”
On McIlroy’s late charge he added: “He played great today – the shot into 15 was true class. He was the one putting pressure on me even though I had those four shots. I think my putt on 17 was a big one.
“Moving closer to Rory at the top of The Race to Dubai is one of my bigger goals. I’m going to try and keep this form going and hopefully I can be up there next Sunday again.”
Earlier Hanson had turned in a two under par 34; then fired a hattrick of birdies from the 11th to leave the rest of the star-studded field trailing in his wake.
One ahead of World Number One Rory McIlroy at the start of the final round, Hanson extended his advantage with a birdie from five feet at the second.
The recent KLM Open winner went four ahead when his playing partner missed from inside five feet at the fourth and fifth, although the US PGA Champion responded with a birdie at the sixth after a sublime tee shot to 15 inches.
Hanson reached the par five seventh in two and two-putted, then holed from eight feet at the 11th to start a run of three successive gains.
McIlroy matched two of them, but the Northern Irishman was four behind with five to play before his late burst.
“I’m a little disappointed,” said the 23 year old. “I'm very happy with the way I played, but I missed a few opportunities on the front nine, I missed four or five short putts in a row.
“I wanted to try to make him work for it. It would have been nice to hole that putt on the last, at least to make him think a little bit, but it wasn't to be and he played well.
“He deserved it. To go out with the lead and play the way he did and shoot 67 is very impressive. He was going to be very tough to beat today.”