LOAN WATCH: Jones can't prevent Cobblers from falling to Saddlers defeat
Callum Morton's first-half double put the Cobblers in charge, but Josh Gordon's header 10 minutes into the second half gave the Saddlers hope.
Danny Guthrie's free-kick evaded everyone to go in with 13 minutes to go, before Rory Holden won it in stoppage time.
Striker Jake Jervis didn't feature as Salford City won 1-0 at Stevenage the same division.
Attacker Josh Neufville came on for the final 10 minutes as Woking drew 1-1 at Notts County in the National League on Saturday.
The Cards led five minutes into the second half through Max Kretzschmar's goal before County levelled as Kristian Dennis netted on 71 minutes.
Sam Beckwith and Corey Panter weren't involved as Biggleswade Town's game with Coalville Town was called off.