Pompey now know for certain they will compete in the third tier of English football for the first time in 30 years next season.
Luke Varney cancelled out Jake Buxton's first-half opener for the hosts but Steve Davies converted the winning penalty to deprive Michael Appleton's side of even the smallest consolation at the end of a torrid campaign.
With Bristol City winning at home to Barnsley, Portsmouth's fate was sealed anyway, but their disappointment will have been compounded by their failure to finish their home campaign on a high.
The game started scrappily, with both sides struggling to retain possession and create any sort of momentum. It was the visitors who were first to threaten, Jamie Ward finding room to fire off a shot from inside the box but Jason Pearce was on hand to block it behind for a corner which Ward wasted.
The Rams pressed again and Theo Robinson's strike produced a routine save from Jamie Ashdown.
Pompey's first chance to apply some pressure came to nothing when Greg Halford fouled Frank Fielding as Scott Allan whipped in a corner.
Allan then had a go himself with an ambitious 30-yard strike which was diverted off course by Jeff Hendrick.
Frank Fielding was finally called into meaningful action on the half-hour mark, scrambling across goal to tip Joel Ward's effort wide.
Derby were soon back on the front foot and when Ward swung in a delivery from the right, Buxton was unmarked to head home from close range.
Dave Kitson's frustration was evident and he was booked for kicking out at the lively Ward on the stroke of half-time. Fellow striker Varney mounted a more constructive response to the setback with a 20-yard shot which Fielding did well to hold onto.
Derby boss Nigel Clough was forced into a change at the break as the injured Fielding was replaced by Adam Legzdins, whose last appearance for the Rams came back in September in the 3-0 win over Millwall.
Legzdins first task was to keep out Varney's shot from outside the area and he was equal to the challenge. The two had a more bruising encounter moments later as Varney caught the goalkeeper in an attempt to get to a loose ball, leaving the former Birmingham trainee requiring a bandage on his head.
With news of the Robins' progress at Ashton Gate filtering through, the home fans tried manfully to rally their side but Ashley Harris' long-range drive never looked likely to threaten as it drifted wide.
Harris limped off soon after with Marko Futacs, scorer of the winning goal in the dramatic 4-3 victory over Doncaster, coming on to replace him.
Allan then fizzed a shot against the crossbar following a powerful run before Portsmouth finally got their reward with 16 minutes to play.
Futacs slipped in Varney and he coolly slotted past the substitute goalkeeper as their personal duel continued.
The hosts' joy was short-lived as four minute later Ward was brought down by Pearce in the box and despite Davies' spot-kick striking Ashdown's legs it still found its way in.
Derby held on to win their final away fixture of a league campaign for the first time in 10 years, but the overwhelming emotion at Fratton Park was one of dejection as Portsmouth contemplated life in League One next season less than four years after winning the FA Cup at Wembley.
