After a goalless first half, Northampton took a deserved lead through Sam Hoskins only for David Ferguson to head Pools level just two minutes later.
Some attacking changes from Challinor shortly after saw substitute Joe Grey deliver a pin-point cross for Luke Molyneux to volley in a late winner.
It confirmed Pools’ 19th win in their last 22 games at Victoria Park and only the second time they have come from behind to secure victory.
Middlesbrough have ‘cooled’ interest in Norwegian ace, Nottingham Forest make ‘opening bid’ for Watford star
Paul Hartley hints at possible transfer breakthrough for Hartlepool United
Middlesbrough transfer news: Boro to battle local rivals for Man City forward, Coventry City play down Everton interest
Hartlepool United complete the signing of ex-Birmingham City and Walsall man
This is why Hartlepool United's ex-Luton Town defender missed Blackburn Rovers defeat
“Absolutely delighted,” Challinor said following the game.
“It's not a good habit to get into winning games from losing positions but to win the game the way we have, has made it all the more special.
"We've had issues imposing our system on teams when they play with a three [up front]. We were miles off it in the first half and were sloppy but we still had the best opportunity in the first half with Dales [Matty Daly] sliding Will [Goodwin] through.
"They score in the second half and we equalise straight away and then you have a choice to continue or make a change and we made changes to have a positive impact and that proved to be the case.
"We scored a brilliant goal and could have scored before that. We had to defend at the end but the way we won it today makes that extra bit special.
Challinor added: "We’ve not been at our best but we’ve shown enough opportunities to win a game. I think Northampton will feel hard done by not to have got something from the game because they are a good side and they made it difficult for us, it was a turgid first half from our perspective.
"But we reacted very well and created the chances after making changes and we can be pleased with how we’ve won today.
"The character is there and the resilience is there in the players, they just need to drag it out when they're on the pitch.
"To win in a way where we've been average from our perspective for 55-minutes but changed things and shown belief is brilliant.”