Michael Collins struck in the third minute of injury-time to earn a third win in four games for Huddersfield and put them 12th in the table.
Collins, who had also scored in three of Town's previous four games, fired home after a backheel from Ian Craney.
Collins was earlier fouled for the penalty which was scored by Gary Roberts to put Huddersfield ahead.
Alex Nicholls equalised from 25 yards and team-mate Jabo Ibehre twice nearly won it before Collins struck.
Huddersfield: Smithies, Butler, Nathan Clarke, Berrett, Holdsworth, Williams (Kamara 74), Craney, Collins, Goodwin, Roberts, Cadamarteri. Subs Not Used: Glennon, Tom Clarke, Jevons, Lucketti.
Booked: Goodwin, Cadamarteri, Berrett, Butler.
Goals: Roberts 26 pen, Collins 90.
Walsall: Gilmartin, Weston, Palmer, Roberts (Boertien 69), Gerrard, Deeney, Hughes (Reich 90), Bradley (Mattis 72), Nicholls, Ibehre, Ricketts. Subs Not Used: Kajtezovic, Smith.
Booked: Ricketts, Roberts, Weston.
Goals: Nicholls 49.
Att: 11,827
Ref: Andy Haines (Tyne & Wear).
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