Players returned to Loch Lomond early Friday to complete the opening round after play was suspended due to darkness on Thursday.
Els was able to get his first round in on Thursday, but he did have to contend with a four-hour weather delay. On Friday, the dismal conditions continued but Els found a bright spot as he prepares to defend his British Open title next week at Royal St. George's.
'I've put myself in a pretty nice position at the moment. Two good days, considering the weather conditions but there are still two days to go,' said Els. 'I've been in this position quite a few times so I know what I have to do. I've got to keep going and try to broaden my lead.'
Els parred his first four holes before his tee shot stopped 12 feet from the cup at the par-3 fifth for his first birdie of the day. He added a birdie at the very next hole and hit is approach inside six feet at the par-4 seventh to make it three in a row.
The South African made the turn at 10-under but found trouble at the par-4 12th. He failed to get up and down for his first bogey of the tournament, however Els regained the shot quickly with a birdie at the par-5 13th.
At the par-4 14th, Els hit his second shot to five feet and ran home the putt for another birdie.
Els, who captured the first two events on the PGA Tour this season and added a pair of European Tour victories early in the year as well, is ready for the weekend and the quest that lies ahead.
'I've been playing close to my best and that's a good sign,' said Els. 'This is an independent tournament on its own. It's the Scottish Open and I will play as hard as I can over the weekend. Is it going to take something out of me? I don't particularly care right now.
'At the start of the year I did all these miles and won tournaments around the world. If that didn't take it all out of me I don't think this will so I don't want to worry about that.'
Fellow South African Tim Clark carded his second straight 68 to finish alone in fourth at 6-under-par 136. Bradley Dredge was one shot further back at 5-under-par 137.
Peter Lonard of Australia shot a 68 to finish alongside England's Ian Poulter and Martin Maritz of South Africa in a tie for sixth at 4-under-par 138.
Darren Clarke was one shot further back after a round of 70. Clarke was joined by Ian Garbutt, David Howell, Gary Murphy, Brett Rumford and Jarmo Sandelin at 3-under-par 139.
American John Daly fired the low round of the day with a 5-under 66 to finish in a group at 2-under-par 140.
The 36-hole cut fell at 3-over-par 145 with 79 players qualifying for the weekend. Phil Mickelson responded from a disappointing opening round with a 68 on Friday to survive.
Defending champion Eduardo Romero was aided by a chip-in eagle at the par-4 14th to make the cut on the number.