Eoin Jess fired over after just eight minutes, before David Hunt hit the post in the 19th minute with an effort that rebounded away to safety.
There was concern for United when Jamie Kearns pulled up after making a good run forward early in the game, and the attacking midfielder had to be replaced by Roni Joe.
After 24 minutes Aylesbury should have taken the lead. Gavin Jaggard was taken down just inside the penalty area, but Drew Roberts' spot-kick was saved. He reached the follow-up, but with the goal gaping slotted his finish wide of the post.
Northampton's new signing Andy Kirk saw a fierce effort superbly tipped onto the bar by Sam Styles, as well as a header which went over the bar. Neil Lazarus then struck a 20-yard shot which was comfortably fielded by Lee Harper, but the football leading up to the effort was excellent from Aylesbury once again.
Half-time: Aylesbury 0-0 Northampton
The interval saw both sides switch goalkeepers, Jack Rashid taking over in goal for Aylesbury and ex-Duck Mark Bunn playing for Northampton.
Paul Edgeworth burst forward from his new central midfield role, but his low drive missed the target.
The Cobblers took the lead just two minutes into the second period. Scott McGleish sprung the offside trap, and fired an unstoppable dipping effort from 20-yards which left Rashid no chance. 1-0 Northampton
Aylesbury's best chance of the game came soon after as they looked to respond quickly. Darran Hay flciked the ball on for Neil Lazarus, who half-volleyed a shot which was well parried by Bunn.
John De Souza and Granville Mellington replaced Drew Roberts and Neil Lazarus as the game lost momentum due to substitution stoppages.
Kirk had another effort go over the bar, before Gary Crawshaw made his much anticipated return to Aylesbury colours, replacing Roni Joe with ten minutes remaining.
Despite a couple of promising touches, he couldn't swing the direction of the game, and Mr Williams blew for full-time, and a 1-0 win to the League Two side.