Johnson completed 8 of 11 passes for 187 yards before giving way to backup Brooks Barden who threw his first touchdown pass.
Johnson threw 6 yards to Trent Bostick for a first-quarter touchdown and 39 yards to Austin Duke late in the second quarter as the 49ers (2-0) went up 24-0 at halftime. Duke finished with 166 yards receiving on nine catches.
The 49ers had 468 total yards to 112 for the Blue Hose, with Presbyterian picking up 85 of its yards in the final quarter.
A 1-yard run by Darrell Bridges with 4:36 remaining provided the only touchdown for Presbyterian (0-2).
AP College Football website: www.collegefootball.ap.org