The Saddlers had looked in total control after two goals from Jabo Ibehre gave them a deserved lead.
The skilful striker accepted a pass from hard working Troy Deeney in the 14th minute and his low shot glanced off unlucky defender Nathan Clarke leaving keeper Alex Smithies no chance of saving.
Walsall might have added a second only three minutes later, but outstanding midfielder Jim Goodwin did well to block a shot on the line from Sofiene Zaaboub.
The Saddlers were playing their best football for some time and it was no surprise when Ibehre struck the ball perfectly into Smithies' bottom right-hand corner from another pass by Deeney in the 28th minute.
Huddersfield had produced little but two minutes before half time Danny Cadamarteri sent in a cross from the right and a shot by experienced striker Booth squirmed under the body of the hapless Gilmartin and an assistant referee signalled that the ball had gone just over the line for a goal.
The Terriers were sparked into action and moments before the interval, Gilmartin failed to go for a corner by Jim Goodwin and the 35-year-old Booth powered a header into the back of the net.
The whole balance of the match changed dramatically with Huddersfield suddenly looking by far the better side.
In the 63rd minute, Walsall's most experienced player, Michael Ricketts, lost control in midfield enabling Goodwin to feed Martin Kelly.
The 18-year-old full-back, who is on loan from Liverpool, sent a great low shot past Gilmartin for the Terriers' winner.
Smithies made a superb 65th minute save, tipping over Ricketts' fierce free-kick, but Walsall rarely threatened after that and the Terriers ran out deserved winners.