Patrick Agyemang proved to be the hero, with goals either side of half time, and the win was sealed by a third from Danny Spiller.
The game, described by Gills chief Andy Hessenthaler as the biggest in a long time, was tight in the opening 45.
Gillingham, though, took the ascendancy on the stroke of half time - with Agyemang heading home from close in after Chris Hope had flicked the ball into his path.
Walsall attempted to find a foothold in the game, with Jorge Leitao and Kris Taylor going close, but they were undone on 65 when Spiller played in Agyemang who kept his cool to stroke home.
Matthew Jarvis and Nicky Southall had chances to extend the lead before Spiller headed home from a corner late on to seal a valuable three points.
