Bantams keeper Scott Loach pulled off two stunning saves to frustrate Lee Richardson's men and the visitors will be cursing their luck after failing to find a way through City's under-pressure defence.
Thorne has now bagged nine goals since the turn of the year and it was no surprise when he headed them in front after 15 minutes.
Stuart McCall rang the changes after City's hard-fought draw at Rotherham and his fresh line-up bossed the game early on.
Winger Joe Colbeck posed plenty of problems with his pace and when he picked out overlapping full-back Ben Starosta after 15 minutes, he supplied a superb cross for Thorne to power in his header from six yards out.
But City failed to make the most of their early dominance and after the interval the visitors came out determined to get back into the contest.
Lively Chesterfield striker David Dowson went down under a challenge from Mark Bower, but referee Colin Webster waived away the penalty appeals and Loach, who had flapped at a couple of crosses, made amends when he blocked another Dowson effort at his near post.
Twenty minutes from time City had a real let-off when Lloyd Kerry's inswinging corner beat everybody in the six-yard box, only for substitute Adam Smith to scoop the ball over the bar at the back post.
Starosta blotted his copybook when his slip allowed Dowson a clear run-in on goal, but Loach came to his rescue with a smart one-handed save.
Chesterfield keeper Barry Roche denied Thorne a second when he let fly from 12 yards and City substitute Barry Conlon saw his free header go over the bar.
The visitors, who have struggled on their travels, piled forward in a desperate bid to grab the equaliser, but Loach would not be beaten and he produced a sensational save four minutes from time to keep out Jamie Winter's 25-yard shot.