John-Joe O'Toole's second half header was enough to see his old side Bristol Rovers lose on their return to the Football League.
Darrell Clarke named a strong side ahead of the opening day test naming summer recruits James Clarke, Chris Lines and Cristian Montano in the starting 11.
Rovers started the game at a fantastic tempo but found chances hard to come by against a solid Northampton defence.
Jermaine Easter did have a penalty claim turned down by referee Mark Heywood following a clash with Cobblers keeper Adam Smith.
Darrell Clarke's men had a massive let off moments later as Tom Parkes attempted a long range header back to Steve Mildenhall only to see Marc Richards latch onto the ball. Top goal scorer for Northampton last season, Richards dragged his shot wide of the goal.
Rovers could and probably should have taken the lead with just over five minutes of the first half to play as Matty Taylor rounded Smith only to lose control of the ball allowing Ryan Cresswell to clear the danger.
Northampton took the lead in the tie five minutes into the second half as left back David Buchanan's flat cross was headed home emphatically by John-Joe O'Toole on his return to the Memorial Stadium.
Darrell Clarke tried to swing the tie in his sides favor introducing both Ellis Harrison and latest addition Jeffrey Monakana before the hour mark.
The second half lacked the tempo of the first with neither side able to break the other down in the beaming sun. Play was disrupted even further when with just over 15 minutes of the game remaining referee Mark Heywood ordered for a drinks break.
Northampton almost doubled their lead with ten minutes of the game to go as a lovely cross field ball from Sam Hoskins fell to Richards but the Cobblers skipper fired low and forced a great save out of Steve Mildenhall at point-blank range.
Rovers tried hard to find a goal and in the final minutes of the game Ellis Harrison was put through onto goal but could only shoot into the arms of Adam Smith.
Up next for Rovers is Championship side Birmingham City if the First Round of the Capital One Cup at the Memorial Stadium on Tuesday night before making the short trip South to take on Yeovil Town next weekend.
Rovers: Mildenhall; Leadbitter, J. Clarke, Parkes, Brown; Sinclair, Lockyer, Lines (C), Montano (Monakana - 60); Taylor (Bodin - 71), Easter (Harrison - 56).
Unused Substitutes: Preston (GK), O. Clarke, Gosling, Blissett.
Northampton: Smith; Taylor, Diamond, Cresswell, Byrom, Richards (C), Adams (Corry - 88), Lelan, Potter (Holmes - 64), Buchanan, O'Toole (Hoskins - 73).
Unused Substitutes: Clarke (GK), McDonald, Clavert-Lewis, Hackett.