Allott was put clear by substitute Tcham N'Toya-Zoa on 83 minutes and finished after the second attempt after keeper Philip Senior parried his first effort with his legs.
But Nottinghamshire-based referee Phil Joslin ruled Allott handled as he tried to control N'Toya's pass and cut short Chesterfield's celebrations.
In injury time Allott raced clear of Huddersfield's defence but with only Senior to beat he dragged a tame shot wide of the left-hand upright from inside of the six yard box when it seemed easier to score.
The introduction of ex-Spireites ace Chris Brandon livened up a tepid encounter that for long periods had been a scrappy affair played mostly in midfield.
Brandon, playing against his old club just weeks after leaving Saltergate on a free transfer, forced visiting keeper Carl Muggleton into a trio of fine saves after replacing Danny Schofield on 68 minutes.
Earlier, veteran Robert Edwards was denied a certain goal against former employers Chesterfield by ex team-mate Steve Blatherwick.
Midfielder Edwards fired in a fine right-footed strike after Steve Blatherwick misjudged Junior Mendes' right-wing cross on 35 minutes.
But rugged centre-back Blatherwick atoned for his earlier error by blocking Edwards' thunderous strike on the six-yard line.
At the other end Spireites striker Caleb Folan had the visitors best chance of the first half when he raced onto Huddersfield defender David Mirfin's misplaced back header on 19 minutes.
The centre forward shrugged off a brave last ditch challenge from Efetobore Sodje to get his shot away but he could only look on in agony as the effort flew inches wide of the target.
The only other serious chance came from Chesterfield's Mark Innes but he shot over from a tight angle just before the break when Allott's cross evaded the home defence.