The Cobblers looked to be heading for a second successive home triumph when Jacob Blyth scored his second goal in three starts to put them in front after half an hour.
The Leicester City loanee powered home a back-post header after some energetic play and a fine right-wing cross from Danny Emerton.
But the visitors showed great spirit to find a way back into the match. First, Derby loanee Callum Ball led a break that saw the ball worked into Karl Hawley to play a pinpoint pass that put Chapell straight through and with just Matt Duke to beat he made no mistake.
Northampton did little to react to the goal, which inspired Torquay to remain on the front foot and pursue a victory that had looked unlikely at half-time.
It arrived when Ball played a crossfield pass to Chapell, who burst inside Joe Widdowson and fired a shot past Duke to settle it.