First-round co-leader Klas Eriksson of Sweden shot 70 for a share of 8-under 136 with Denmark's Anders Hansen (68) and Spain's Jose Manuel Lara (69).
Colin Montgomerie, who missed the cut last week in Dubai, headed into the weekend only four strokes off the lead after posting a 3-under 69. He was tied with fellow Scot Stephen Gallacher (68) and Frenchman Jean-Francois Remesy (69) for fifth place at 7-under.
Scott, one shot back after 18 holes, staked his claim to the top spot Friday with birdies at the first, fourth and seventh holes to get to 8-under par. Although his scoring stalled with seven straight birdies from the eighth to the 14th, Scott soon vaulted to 10-under with one stroke of his 5-iron.
His drive ran through the fairway at the 466-yard, par-4 15th, the most difficult hole at Doha Golf Club. Left with 200 yards in from the first cut of rough, Scott flushed his approach with a 5-iron, then watched his ball hit the center of the green and roll in the hole for an eagle two.
'You need a little bit of luck now and again because I certainly didn't expect it to go in,' said Scott. 'I was saying to my caddie the other day that it has been about five years since I holed a full iron shot like that in play, so perhaps I was due one.'
He failed to birdie the 16th when he missed a putt from 18 feet, but sank a 15-footer at the 17th for his final birdie in a bogey-free round.
Scott, who won the 2001 Alfred Dunhill Championship for his first professional title, averaged 25 putts per round over the first two days. He putted 26 times in the first round and just 24 times on Friday.
'I can't control what other players are going to do,' he said. 'But if I keep playing the way I have over the first couple of days then I think it will be good enough.'
Argentina's Eduardo Romero (67), Welshman Ian Woosnam (69) and defending champion Tony Johnstone (70) of Zimbabwe were part of a 10-man logjam at 6-under par.
Joakim Haeggman, the other Swede to lead after one round, turned in a 1-over 73 and tumbled into a tie for 18th at 5-under 139.
Former Qatar Masters winners Andrew Coltart (1998), Paul Lawrie (1999) and Rolf Muntz (2000) made it to the weekend. Coltart and Muntz finished the day at 2-under par, while Lawrie made the cut on the number at 1-under 143.
Full field scores from the Qatar Masters