Scott, who set the course record, completed the tournament at 20-under-par 268. Mark Pilkington and Robert Karlsson had set the old course record of 63 in 2001. Scott's total of 268 matched the tournament record that Paul Lawrie set in 1999.
'Well today was pretty special,' said an understated Scott. 'It didn't feel any different than any other day, but everything was going the right way. Right from the first green, rolling in a nice 15-18 footer there, it just went right in the middle. Everything was feeling good from there and I just ran with it.'
Scott, who also won this crown in 2002, collected his sixth European Tour win, but his first since the 2005 Johnnie Walker Classic.
The 61 was a personal best for Scott and was one stroke off the European Tour record. His previous best on the European Tour was 63, which he shot four times. On the PGA TOUR, Scott has carded four 62s.
'It's days like these that get your juices going,' Scott said. 'To go out and shoot 61 is certainly, under the conditions, the best-ever round.'
Scott's final two-round score of 126 was two strokes shy of the best closing 36 holes in European Tour history.
Henrik Stenson, the 2006 champion, gave Scott a run for his money as he closed with a 7-under 65 at Doha Golf Club, but it was only good enough to finish three back at minus-17.
Charl Schwartzel was two strokes further back at 15-under-par 273 after a final-round, 5-under 67.
Third-round leader Johan Edfors managed a 2-under 70 to end alone in fourth at minus-14. Lee Westwood matched Stenson's 65 to take fifth at minus-13. That was Westwood's fourth straight top-5 finish dating back to the 2007 season.
Scott got off to a flying start as he opened with a birdie on each of the first five holes. His birdie at the third gave him a share of the lead, while the birdies on four and five moved him two clear of Edfors.
'It's not the first time I've had a run, but for a Sunday of a tournament in contention it was a nice feeling to get out there and get the lead early,' Scott stated. 'I always like to consider myself a player who is not afraid of taking it deep and when you're on those runs you've just got to go with it.'
The Australian parred the sixth for the fourth straight day, but came back with a birdie on the seventh to get to 15 under.
Scott parred his next two, then birdied 10 and 11. Both of those birdies kept him two ahead of Stenson, who had birdied the ninth and 10th playing one group behind the leader.
He birdied the par-4 12th, then carded a pair of pars. Scott then birdied the 15th for the second straight day to take a four-shot lead. That birdie also got him to 10 under for his round.
With a chance at shooting 59, Scott parred the 16th and birdied 17 to get to 20 under. Needing an eagle at the par-5 18th to shoot 59, Scott only managed a par, but it was enough for a three-stroke win.
Stenson, who was searching for his seventh European Tour win, carded a bogey-free round of his own to keep the pressure on Scott.
The Swede ran off three birdies in a four-hole span from the third to jump to 13 under, where he trailed by two.
Stenson connected on back-to-back birdies from the ninth to remain two back. His challenge slowed as he parred four straight holes from the 11th. He birdied 15 and 16, but each was only good enough to keep him three back.
Needing a birdie and an eagle over the last two holes, Stenson managed to par both to finish three behind Scott.
'I'm delighted. I had a good finish in Abu Dhabi due to a good short game and good putting and I kept that going this week,' Stenson said. 'I tried my hardest. There is not much you could do about what Scott did.'
Edfors, a three-time winner during the 2006 season, was just 1 under after eight. However, he stumbled to bogeys on the ninth and 10th to slide to 11 under, where he trailed by six.
He ran off three birdies in a four-hole span from the 13th to get back to 14 under, but parred the last two to end alone in fourth.
Colin Montgomerie closed with his second straight 3-under 69 to take sixth at 11-under-par 277. Christian Cevaer, Nick Dougherty, Sergio Garcia, Jyoti Randhawa, David Howell and Anton Haig were one shot further back at minus-10.