France's Jean-Francois Remesy shot 68 to finish the day alone in second place at 11-under, while Scotland's Colin Montgomerie bogeyed the final hole to fall back into a tie for third at minus-10.
Scott, in search of his second European Tour title, increased his advantage to five strokes with four birdies through 10 holes. He dropped a shot at the 12th, however, when his approach with an 8-iron flew over the green and he couldn't convert the up-and-down to save par. It was only his second bogey of the tournament.
The 21-year-old Australian settled for pars the rest of the way, even at the 18th. Although he left himself a four-foot putt to birdie the par-5 closing hole, Scott's ball clipped a spike mark and slid by the right side of the cup.
'It would have been nice to make that one at the last but overall it is a good result,' said Scott, who notched his breakthrough victory by capturing the Alfred Dunhill Championship in his first start of 2001. 'I had the chance to run away with it because I played beautifully on the front nine.'
Scott, who surrendered a five-shot, third-round lead to Peter O'Malley at last year's English Open, said he feels better equipped to deal with the pressures that come with taking a lead into the final round.
'I think last year it was all pretty new. When I was ahead I tried to force it a little bit too much,' he said. 'But I think I am a stronger player than I was then with a year's more experience under my belt. Tomorrow I will go out and try to be comfortable straight away, get a putt going in or something like that to get relaxed and get into a good rhythm.
'It's nothing you can force, you've just got to let it happen and I think my time has come.'
Remesy was four back of Scott after round two but lopped one stroke off that margin with an active round Saturday. Suffering from back pain that flared up late in his round Friday, the 37-year-old Frenchman fought through the discomfort to card six birdies, including four on the back nine, against two bogeys.
'I still had to take some precautions with my swing and not hit quite as hard through the ball as normal,' said Remesy, whose lone win came at the 1999 Estoril Open in Portugal. 'I also had to be careful when I was bending down to mark my ball or pick it out of the hole. But fortunately, it didn't go against me, so we will see what happens tomorrow.'
Montgomerie, the seven-time Order of Merit winner with 26 victories to his credit, rang up his sixth birdie of the day at the 16th to close within three shots of the lead. He ended on a down note with a three-putt bogey at the 18th to complete his second straight round of 69.
Nineteen-year-old Nick Dougherty, a protege of fellow Englishman Nick Faldo, had a 68 to join Monty in third place. Rounding out the quartet at 10-under 206 were Spain's Miguel Angel Martin and Stephen Gallacher of Scotland.
England's John Bickerton, Denmark's Anders Hansen and defending champion Tony Johnstone of Zimbabwe finished five shots off the pace at 9-under.
Full field scores from the Qatar Masters