Jon Guthrie put Northampton ahead when Newport failed to clear Mitchell Pinnock’s free-kick and the centre-back gleefully slammed home.
Jake Cain almost had the Exiles level early in the second half but his free-kick whistled just past the post.
But it needed a fine close-range save by Joe Day to prevent Nicke Kabamba from doubling Northampton’s lead.
Newport’s miserable night was compounded when they lost defender Scot Bennett to a worrying looking injury with 18 minutes of normal time remaining.
“I thought we were absolutely awful first half, gave it a go first half with a better team but never really looked like scoring.
“A few have played themselves out of the squad completely, some of the performances tonight were dreadful… but I pick the team and I’ll take this one on the chin.
“I don’t at the minute [know the severity of Scot Bennett’s injury] and that’s probably summed the evening up, because he’s a key player for us. I just hope it’s not a bad one.”
