Mathias Doumbe gave the Cobblers an early lead but they were soon pegged back by Michael Timlin's strike.
Chris Hackett netted from Emile Sinclair's cutback just before the hour mark to make it three victories in four games for revitalised Northampton, who are now five points adrift of safety.
"It was a tight game against a very good side and it had a little bit of everything really," said Wilder.
"Southend surprised us with their shape at first and they didn't allow us to play at all in the first half.
"But we got to grips with it and I thought we got better as the game went on. The substitutes we brought into the game managed to put them under a bit of pressure, too.
"Gradually we wore them down and we could have nicked another one in the last 15 minutes of the match but it's a great effort and a very good result for us.
"We got the crowd off their feet with our committed performance and that is always pleasing as a manager."