The 21-year-old Australian collected seven birdies and an eagle for the narrow advantage over Jos Maria Olazbal, Paul McGinley and local professional James Stewart.
'I'm very happy,' said Scott, who is seeking his second European Tour title after winning the Alfred Dunhill Championship in South Africa nearly a year ago. 'I got off to a really good start and after the three opening birdies, it went from there.'
Scott bogeyed the par-3 fifth but rang up another trio of birdies from the ninth to the 11th. He capped the streak with an eagle after knocking a 2-iron to 15 feet at the par-5 12th.
After dropping a stroke with a bogey at 15, Scott made his way in with a birdie at the 17th and a par at the last.
Olazbal, who finished second to Jarmo Sandelin at last week's BMW Asian Open, carded seven birdies in 12 holes to grab a share of the top spot, only to send his final drive into the woods en route to a closing bogey and a 65.
McGinley, the runner-up in the season-ending Volvo Masters, and Stewart each had seven-birdie, one-bogey efforts, as well.
'It's a great feeling,' said Stewart, 26, the club champion at Hong Kong Golf Club in 1995. 'After making the cut in Taiwan last week, it gave me a lot of confidence.'
Among the 13 players deadlocked with 5-under 66s were Michael Campbell, European Q-School graduate Matthew Cort of England and 1999 Hong Kong Open winner Patrick Sjland.
Englishman Simon Dyson, the defending champion and the winner of the 2000 Asian Tour Order of Merit, finished the day three shots off the pace after a 67. Sandelin was in the next group at 3-under.
The Hong Kong Open, which began in 1959, is being co-sanctioned by the European Tour and Davidoff Tour for the first time. This is the second event to count toward the 2002 European Tour Order of Merit and the season-ending tournament on the 2001 Davidoff Tour.
Full-Field Scores from the Omega Hong Kong Open