He finished 54 holes at 14-under 199 and is one shot clear at the TPC Wakefield Plantation.
Rich Barcelo also shot a 65 in round three and moved into second place at minus-13, followed by Jim McGovern, who, like the men above him on the leaderboard, carded a 65 and came in at 12-under 201.
Johnson played well almost immediately on Saturday. He tallied birdies at two and four to reach 10-under par for the championship, but he got to the top of the leaderboard with his play right before the turn.
Johnson made back-to-back birdies at eight and nine and was suddenly among the leaders at 12-under par. He parred his next three, but birdies at 13 and 14 gave him sole possession of first place.
He parred his last four, but it was enough to keep Johnson atop the leaderboard.
'I hit it solidly all day and had good chances on every hole,' noted Johnson. 'You know, I've been playing well and just kind of 'hanging in there' all week and season, so it feels great to have it come together on a day like this.'
Johnson is the most experienced winner in the group near first place. He owns four Nationwide Tour wins, with the most recent coming at the 2006 Wichita Open. If he can hang on Sunday, Johnson would move into a tie for fourth place for most wins in Nationwide Tour history.
Chris Baryla fired an 8-under 63 in Saturday's first group. He jumped up 54 places into a tie for fourth place with several players at 11-under-par 202.
Chad Collins (64), Josh Teater (64), Adam Bland (66), Cameron Percy (66), Grant Waite (67), David Mathis (67), Josh Broadaway (68) and second-round co-leader Jeff Gallagher (69) joined Baryla at minus-11.
The remaining overnight leaders struggled badly on Saturday.
Bradley Iles shot a 1-over 72 and fell into a tie for 24th at minus-8. Jeff Curl managed a 3-over 74 and is in a group tied for 39th at six-under 207, while Scott Gardiner posted a 5-over 76 and is down to 53rd place at minus-4.