'Even if it was one ahead I would have taken it because it is an advantage over everybody else,' said Scott.
Scott, who broke the previous 54-hole tournament record by two shots, has built a commanding lead with one round to play in search of his second title of 2002. Scott's first victory came at the Qatar Masters, a six shot win over Nick Dougherty and Jean-Francois Remesy.
The rainy conditions that plagued the PGA Centenary Course at The Gleneagles Hotel continued throughout the day. Scott, who faired well in the rain on Friday, struggled early Saturday but managed to hold on in the end.
The Australian began the day with a four shot lead but watched as back-to-back bogeys from the third dropped his advantage to one. Scott recovered with an 18-foot birdie at the seventh to reach 11-under but was soon joined atop the leaderboard.
Russell, who was six shots off the pace to start the round, made an early charge with four birdies on the front nine. The Scot hit his approach to six feet at the 11th for birdie to grab a share of the lead.
Scott was intent on keeping the lead to himself, however, and birdied the eighth to move to 12-under. Moments later, Russell ran home a birdie at the 12th to match Scott once more.
Scott took the outright lead with his third birdie in a row at the ninth but stumbled with a bogey at the very next hole to again share first.
The 22-year-old Aussie began to shine on the inward half and knocked his third shot from the rough inside three feet at the par-5 12th. Scott drained the birdie putt and never looked back.
He reached the green in two at the par-5 16th and rolled in a 12-footer for eagle to open a three shot lead. Scott birdied the following hole and ended his round with an eight-foot birdie at the last to stand five clear of the field.
'Fortunately there are par-5s late which is always good,' said Scott. 'Finishing like that makes it hard for the other guys because they have a lot to think about tonight and I just have to think about getting in a good rhythm tomorrow.'
Gardiner used a remarkable finish to grab a share of second alongside Russell at 12-under-par 204. Gardiner birdied five of his last six holes for a round of 65.
Sam Torrance, who celebrated his 49th birthday Saturday, posted a 3-under 69 that included an eagle at the par-5 16th, to finish alone in fourth at 10-under-par 206.
Fredrik Andersson and Matthew Cort each carded rounds of 70 and are tied for fifth alongside first round leader Richard Green at 8-under-par 208.
Rolf Muntz fired the low round of the day with seven birdies and an eagle. Muntz could have matched the course record but a late bogey left him with a 64, one shy of the mark. Muntz was joined by Stephen Dodd, Jeremy Robinson and Marcel Siem in a tie for eighth.
Full-field scores from the Diageo Scottish PGA Championship