Despite going behind to Zander Diamond’s first-half opener, Stevenage hit back through goals from Chris Whelpdale and Walton before Ryan Cresswell was sent off for the visitors.
Home skipper Bira Dembele headed Dean Parrett’s free-kick wide in the opening ten minutes before Northampton goalkeeper Matt Duke palmed away a fierce effort from Chris Beardsley.
Northampton edged ahead againt the run of play on 39 minutes when defender Diamond met Joel Byrom’s free-kick at the back post with a half volley into the bottom corner.
Stevenage continued to press after the break and equalised on 65 minutes when Parrett found space on the edge of the box and clipped a ball to the back post for Whelpdale to head in his first goal since Boxing Day.
Chris Day denied John-Joe O’Toole in the dying moments to allow Stevenage to break forward and Walton to turn in a 90th minute winner after coming on from the bench.