Danny East's early goal was enough to secure a fifth straight win for Andy Awford who made eight changes to his starting line-up at Sixfields.
Trevor Carson, Jed Wallace and Nicky Shorey were the only players to remain from the team that started the 3-2 victory over Bristol Rovers. Daniel Alfei, Joe Devera, Sonny Bradley, Johnny Ertl, Danny East, Wes Fogden, Jake Jervis and Patrick Agyemang were all given their chance to impress although Ben Chorley was absent due to his wife giving birth.
Awford's gamble paid off early on as Pompey took the lead after just six minutes. Jervis flicked a free kick to East who ghosted into the box amd hooked the ball past Matt Duke to give over 1,300 travelling fans plenty of reason to cheer, especially as Bristol Rovers had lost earlier in the day to confirm Portsmouth's safety.
Pompey dominated possession in the early stages of the half with some flowing football that had Northampton chasing shadows for a while. However, they eventually got a grip of the game and began to pose problems for the makeshift defence they were up against.
The visitors received a huge let off when an unmarked Emile Sinclair failed to connect with Evan Horwood's swinging cross when he really should have scored.
The pressure built and ex-Pompey loanee John Marquis forced an excellent save from Carson at the near post and then somehow managed to stop Darren Carter's close range effort from finding the back of the net.
Those Pompey fans who thought that their team would regroup after the break were mistaken as Chris Wilder's team virtually dominated the second half and wasted so many chances to equalise.
Ivan Toney was guilty of one of the worst misses as he somehow managed to strike the ball into the ground and over the bar from twelve yards.
John Marquis had a hat-trick of chances to score as the defence failed to track him but, as with his time at Portsmouth, his finishing was woeful and Pompey were let off the hook.
The ball kept coming back into dangerous areas for Pompey as Carson's kicking left a lot to be desired and the referee was eager to award dangerous free kicks to the Cobblers but the defence held firm and was well marshalled by Carson when it mattered.
Pompey could have finished Town off when they were caught out by a quick counter-attack but Duke was quick and alert enough to block Wallace's strike.
Northampton threw everything at the Blues in the last minutes but Bradley and Devera dealt with the long balls into the box and that early goal from East proved to be enough for yet another win.
Unlike Pompey's previous wins which were well deserved, most fans would accept that they were lucky to escape Sixfields with all three points, but with eight changes made what more would you expect?
Out of those who came in, Ertl was fairly impressive with his passing and his workrate and Devera and Bradley showed how dominant they could be in the air, although their slack marking ability was highlighted. East scored but faded, whilst Agyemang never looked like lasting the entire match.
The main disappointment was Jake Jervis who has scored some important goals for Pompey this season but nothing went right for him today. His touch was poor and he was wasteful when he did have the ball at his feet.
It'll be interesting to see how many of these players Awford will stick with for the trip to Bury on Saturday. You would expect Jack Whatmough and Ryan Taylor to be involved again but who else he picks would be anyone's guess.
For the time being, it's just good to know that Portsmouth are certain to be in League Two next season and can finish this season with a flourish.
Pompey Player Ratings
Trevor Carson: 7 - Kicking was poor bt made some vital saves and kept his composure under pressure.
Daniel Alfei: 6 - Wasteful with his crossing but did defensive duties well.
Sonny Bradley: 6 - Dominant in the air but struggled to mark players.
Joe Devera: 7 - Showed some good ability on the ball rather than simply hoofing it at times. May well play again on Saturday.
Nicky Shorey: 6 - Solid enough.
Johnny Ertl: 7 - Arguably his best performance of the season.
Danny East: 6 - Well nicked goal but faded as the game went on.
Jed Wallace: 6 - Worked hard but should have scored late on and never had much time on the ball.
Wes Fogden: 6 - Chased everything.
Jake Jervis: 4 - Not his day.
Patrick Agyemang: 6 - Worked hard, showed some good touches but didn't have enough of the ball.
Substitutes
Phil Smith
Adam Webster
Bondz N'Gala
Rhys McCabe
Danny Hollands (Jervis 54): 6 - Shored things up.
Ricky Holmes (East 78): N/A - Never really saw the ball.
Michael Drennan (Agyemang 65): 6 - Had a rare shot on target and played the ball to Wallace where he should have scored.