Jack Hamilton's first-half penalty was enough to hand Neill Collins his first league win as Raith Rovers manager at the expense of high-flying Falkirk.
Dylan Easton was brought down by Liam Henderson inside the box, with Hamilton stepping up to power home the spot-kick.
Falkirk failed to trouble Kevin Dąbrowski as the clock ticked down, leaving John McGlynn's side to face a first loss since being promoted back to the Championship this summer.