Chris Doak, ranked No. 341, was the surprise leader at the halfway stage of his home event after a second straight 66 left him at 12-under 132.
Matthew Southgate (64) was in a tie for second place with Ross Fisher (65), Peter Uihlein (66) and JB Hansen (65) a stroke back.
Conditions were ripe for low scoring on the Castle Stuart links but Els foundered on the greens and could shoot only a 2-under 70 to miss the cut a week before he defends his British Open title.
Mickelson, another four-time major winner, was tied for third after his first-round 66 but dropped back into a tie for 13th after a 70.
''I had no idea on these greens – I'm glad I'm leaving,'' said Els, who still felt his game is in good shape heading to Muirfield.
That put the Indian on 3 under – a shot below the cut, which was the lowest this season on the European Tour.
It leaves Mickelson as the biggest draw for the galleries for the final two rounds and he said he is poised to make a charge in his bid to capture his first title on links.
''I was just a little bit off,'' said the eighth-ranked American, who started off with a bogey for the second straight round but wowed the crowd with a wonderful lob shot onto the third green to set up one of his four birdies. ''But I'm in a position where if I get a hot round, I can make up the ground.''
The last Scot to win his national Open was Colin Montgomerie in 1999 – but Doak has a great chance to end that barren run.
Wearing his signature flat cap in honor of his idol Ben Hogan, the 35-year-old Glaswegian thrilled the locals on a sunny, calm morning by the Moray Firth by making three birdies in the first six holes and then adding two more as well as an eagle 3 at No. 12.
He has flitted between the European Tour and second-tier Challenge Tour in recent years, but his resume is littered with triumphs on the Highlands links in his younger days. And he gained confidence by qualifying for last month's U.S. Open.
''That experience all in all was great and spurs you on to get back there,'' said Doak, one of 19 Scots in the 156-man field.
Likewise, Southgate is in uncharted territory after his 64, the lowest round of the week. But he is a dangerous links player owing to his membership at Carnoustie – arguably the toughest of the nine courses on the British Open rota – that he was given for a birthday present as a 16-year-old.
''Every player needs a big break – this could be mine,'' said the 24-year-old Englishman, who worked in a snooker hall six years ago to pay his way as his golf career struggled to get going.
''Where other people may feel a bit uncomfortable bouncing it 20 yards short of the green or hitting this little shot, that little shot, I just step up, see it and play it. It's a shame we don't play more links golf. If the wind picks up, I'll take that.''
Els was a late entrant into the tournament as he sought some links practice ahead of Muirfield, where he won the British Open in 2002 and where he will defend the title captured last year at Lytham.
Off the tee, the South African has played solidly this week but he has struggled on the greens and some of his approach shots haven't been up to his usual standard. He doesn't, however, see this as a problem ahead of next week and his shot at a third claret jug.
''These courses are so different. Muirfield is a lot more traditional links,'' Els said. ''I got a lot of awkward bounces this week but I feel I'm swinging well, striking the ball well.
''I think my game is where I want it.''