A freak strike by top scorer Jorge Leitao helped improve Walsall's chances of staying in Division One with the win described by relieved Walsall boss Colin Lee as "a massive result".
Leitao knew little about it as the ball cannoned off his shin and flew into the net past the stranded Vince Bartram.
Walsall survived intense Gillingham pressure towards the end and stand in goalkeeper Gavin Ward, who had a fine game, had his woodwork to thank for keeping out Mamady Sidibe's effort, set up by 16-year-old substitute Akwasi Edusei.
The defeat, Gillingham's seventh at home this season, extended their run without a win to five games and came at the end of a difficult week which saw joint first-team coach Richard Hill made redundant.
Add to that a long list of injuries to key players, including himself, and that's why Andy Hessenthaler threw in the kids in Gillingham's last home game on a Saturday this season.
Walsall beat Gillingham 1-0 last November but needed the victory to give themselves the chance of avoiding being sucked into the dogfight at the bottom of the table.
Neither side created very much in an ordinary first half but Sidibe missed a great chance on the stroke of half time firing over from inside the six-yard box.
Leitao's goal that eventually decided the game came early in the second half and Gillingham threw everything at Walsall but with Ward denying them time and again all their effort was in vain.
Youngster Spiller made the most of his opportunity in the absence of more experienced players including skipper Paul Smith, whose ever present run in the side this season was ended by the birth of his second child overnight.
Gillingham's best chance of snatching a point came when Tommy Johnson saw his effort kept out by Ward midway through the second half but Walsall lived on their luck.
The Saddlers suffered two injury worries with Ian Roper and substitute Danny Hay both limping away at the end.
Hesenthaler said: "It's been a difficult week but difficult decisions have to be made if the club are to stay out of trouble.
“I was pleased with Danny Spiller, who I thought was absolutely outstanding and on another day we might have won the game."