Freeman sent off as Blues lose to champions.
Pompey will host Plymouth in the first leg of the play-offs on Thursday evening after losing 2-1 to Northampton.
The champions took the lead through Jack Whatmough’s unfortunate own-goal in the opening stages.
Kieron Freeman then received his marching orders for a late challenge, only for a Kal Naismith stunner to draw the hosts level.
A series of attacking substitutions were made as the Blues searched for a winner, but instead James Collins secured all three points for the Cobblers.
Paul Cook made five changes from the side that won at Hartlepool the previous week.
Whatmough was handed his first start for more than a year in the centre of defence, with fellow academy graduates Brandon Haunstrup and Ben Close also featuring.
Ben Davies returned and skippered the side in place of Michael Doyle, while Adam McGurk came in up front.
Meanwhile, former Pompey players Ricky Holmes and John Marquis led the line for the visitors, who were afforded a guard of honour as they entered the pitch.
There were a plethora of awards handed out before kick-off, with Ben Davies picking up six from various supporters’ groups.
But it was Doyle who was named The News/Sports Mail Player of the Season – and the reaction from the fans indicated that it was deserved recognition.
Both sets of supporters then paid their respects to all the Blues fans who have sadly passed away over the past year with a minute’s applause.
Once the action got underway at a warm and sunny – and packed – Fratton Park, it was the visitors who looked more threatening.
Whatmough had to deal with a couple of dangerous crosses as a new-look Pompey side struggled for fluency.
But they were not too far away from opening the scoring on 12 minutes, with Adam McGurk flinging himself at Naismith’s cross and not quite making a clean connection.
Almost immediately, however, they found themselves behind as Whatmough inadvertently sliced Nicky Adams’ cross into his own net.
Pompey were not really playing with a recognised striker, as Gary Roberts occupied a ‘false number nine’ role, flanked by Naismith and McGurk.
They did start to create more as the half progressed, though, with McGurk curling a shot over and Naismith steering narrowly wide.
But Northampton still looked dangerous themselves and Marquis might have done better than firing wildly over after being picked out by Holmes.
Pompey should have been level on 33 minutes following a good move that started with a poor clearance from Cobblers keeper Adam Smith.
Roberts picked the ball up and it soon found its way, via Freeman, to Davies down the right flank.
The full-back sent in a low cross, but Smith redeemed himself by somehow denying Naismith from point-blank range.
Roberts then collected a lovely pass over the top from Close and spotted Smith off his line, although he could not quite chip the ball over the back-pedalling keeper.
Both sides picked up a booking before the break, with Davies and Lawson D’Ath penalised for fouls on Holmes and Haunstrup respectively.
Northampton Town 1
Pompey’s hopes of getting anything from the game were dealt a massive blow just after the restart when they were reduced to 10 men.
Freeman slid in to try to win the ball and although he did not really catch John-Joe O’Toole, referee Mark Brown decided it was dangerous.
He immediately brandished a red card to rule the on-loan Sheffield United utility man out of the play-offs.
But the hosts found themselves level just seconds later – thanks to a strike right out of the top drawer.
There did not look much on when NAISMITH advanced goalwards, but he hit a stunning, swerving 35-yard strike that arrowed into the net.
Cook was forced to make his first substitution on the hour mark, as Close limped off to be replaced by Adam May.
Haunstrup then had the ball in the back of the net, but Brown had already blown his whistle for a foul on Smith by McGurk.
Northampton soon enjoyed a period of pressure, with Marquis denied by Brian Murphy before Alfie Potter fired into the side netting.
Cook made an attacking switch on 69 minutes, as Conor Wilkinson replaced Whatmough for his debut.
That resulted in a defensive reshuffle which saw Gareth Evans drop to right-back and Davies move into the centre.
And Naismith was soon employed at left-back when Haunstrup made way for Ben Tollitt on 77 minutes.
Pompey now had an abundance of attack-minded players on the pitch, but the visitors soon made their numerical advantage count to retake the lead.
Cobblers skipper David Buchanan swung the ball into the box and Collins got a faint touch to turn it home.
Naismith tried to draw the Blues level with another attempt from long-range, but this time Smith dived across goal to make the save.
And Pompey were unable to find a late leveller as the visitors secured victory to cap a memorable campaign.
But plenty of fans still stayed behind to salute the Blues as they returned to the pitch after the final whistle for a lap of appreciation.
Pompey (4-3-3): Murphy; Davies (c), Whatmough (Wilkinson 69), Barton, Haunstrup (Tollitt 77); Freeman, Close (May 60), Evans; McGurk, Roberts, Naismith
Goals: Naismith 48
Sent off: Freeman
Booked: Davies, McGurk, Evans
Subs not used: Jones, Stevens, Doyle, Oxlade-Chamberlain
Northampton (4-4-2): Smith; Lelan, Diamond, Prosser, Buchanan (c); D’Ath (Hoskins 80), O’Toole, Rose, Adams (Potter 62); Marquis (Collins 67), Holmes
Goals: Whatmough 13 (og), Collins 81
Subs not used: Clarke, Cresswell, Taylor, Byrom
Referee: Mark Brown
Attendance: 18,746 (2,807 away fans)