Accrington keeper Ian Dunbavin saved an 89th minute Jamie Lowry penalty but Small struck in the second minute of added time, converting Donal McDermott's left-wing cross from close range.
Spireites forward Small had two good chances to put Chesterfield in front but could not get the better of Ian Dunbavin. The Stanley goalkeeper was quickly off his line in the 21st minute to save at the feet of Small and then clawed out a shot from the striker seven minutes later.
Accrington moved the ball around well without really threatening and it was the home side who almost took the lead in the 43rd minute when Darren Kempson hooked a Jamie Lowry cross off the line.
The visitors wasted a good opening when Bobby Grant fired over after an hour and Tommy Lee rescued Chesterfield with a double save to deny Jimmy Ryan and Billy Kee in the 65th minute.
Small was tripped by Dunbavin in the last minute of normal time, only for Lowry to fire the spot-kick at the keeper, but the Chesterfield striker had the last word.