Added to the League Cup victory at Ipswich in midweek it means a solid start to the season for the Cobblers who struck early at the Recreation Ground and held on well to their lead.
"We are very pleased with our efforts," boss Gary Johnson told the official NTFC website.
"We came out of the block well, we scored early and then had two other chances to extend our lead."
Opposite number Dean Holdsworth felt his side deserved something from the game for their second-half display.
He told his club's website: "We’ve knocked on the door and hit the woodwork two or three times and we were camped in their [Northampton’s] half."