Johnson, at No. 6 on the money list already assured a 2008 PGA TOUR card, had a 16-under 197 total on the Barona Creek Golf Club course.
'I'm surprised to be where I am,' Johnson said.
He had a quadruple-bogey 7 on No. 11 and bogeyed No. 12.
'I played mostly solid except for two holes,' said Johnson, the Mark Christopher Charity Classic winner last month in Rancho Cucamonga.
The top 25 on the money list after the tournament will earn PGA Tour cards, with Scherrer (67) fighting to move up from No. 27.
Kelly Grunewald (67), Jim McGovern (68) and first- and second-round leader Michael Letzig (73) were two strokes back at 14 under. Letzig began the week 26th on the money list, McGovern was 45th and Grunewald 55th.
Letzig three-putted from 3 feet on No. 18 for a triple bogey.
'I tried to tap it in three times,' Letzig said. 'I'm not really sure what happened. The good thing is I'm not out of it.'
Grunewald needs a victory to advance to the PGA TOUR.
'It was a bonus for me to be here this week,' Grunewald said. 'Last week, I was looking at going to first or second stage of Q-school. I'm playing with a lot of confidence and that's what you have to do out here.'
Johnson has been in the final group five times this season.
'I think someone is going to go low,' Johnson said. 'I hope it's me.'