Garath McCleary returned to the starting line up in the place of Adam Wallace in the Slough attack but could not find a breakthrough on the day.
Folkestone were looking dangerous with high balls into the area with Ellis Remy's height causing the Rebels backline a lot of concern and it was a lofted ball which led to the away side opening the scoring.
A free kick was delivered in from the right to the back post from Kevin Watson and Adam Flanagan rose higher than Jamie Jarvis and thumped a header through Kieron Drake and into the net.
A quiet half saw Folkestone take their narrow lead into the interval.
Drake was tested in the game's opening chance of the second half turning a low drive around his left hand post.
Slough saw a Steve Daly header well saved by Tony Kessell before Folkestone extended their lead with ten minutes left. Steve Norman's inswinging near post corner was taken back over the line by Drake with four players all attacking the ball and the goal was given.
Folkestone Invicta Line up
Tony Kessell, Kevin Watson, Steve Norman, Adam Flanagan, Friend, Samuel Okikiolu, Michael Everitt, James Everitt, Ellis Remy, Mark Saunders, Paul Jones. Subs: Ben Sly, Joe Neilson, Lee Shearer, Stonebridge.