Steve Davies' first goal for over a year, on his first start of the season, looked to have put the Rams on course for a much needed Championship victory.
But Nugent fired home a minute from time to thwart Nigel Clough's side.
Portsmouth manager Steve Cotterill was sent to the stands at half-time for comments made to referee Neil Swarbrick and, despite their late rally, the south-coast club have not posted a win in their last 10 games across all competitions.
There was a distinct lack of quality in the opening exchanges, with both sides showing why they have been on such poor runs.
Portsmouth should have made the visitors pay for some indecisive defending 13 minutes in, but Greg Halford's strike took a deflection away for a corner.
Nugent broke clear of the Derby defence after 20 minutes but his scuffed shot was palmed wide by goalkeeper Stephen Bywater.
Derby took the lead after 34 minutes with their first shot on goal.
Tomasz Cywka did well down the left and picked out Davies, and the former Tranmere man gave home goalkeeper Jamie Ashdown no chance with a clinical left-footed volley into the top left corner of the net.
The goal clearly gave the Rams the confidence they have been lacking in recent weeks and they had the upper hand in the remainder of the first half, with Stephen Pearson causing problems down the left.
Portsmouth boss Cotterill was unable to take his place on the touchline for the second half after being sent to the stands for comments made to referee Swarbrick at the break.
Nugent had another chance after 64 minutes but the former Preston striker fired over the bar from just six yards out.
Portsmouth brought on veteran striker Nwankwo Kanu with just over 20 minutes remaining in a bid to salvage something from the game.
The home supporters were growing increasingly frustrated as their side huffed and puffed but struggled to break Derby down.
Portsmouth pressed forward in the closing stages but Clough's side stood firm, with skipper Shaun Barker and Miles Addison solid at the heart of their defence.
But just as it seemed as though the visitors were going to hold on for three precious points, the home side levelled a minute from time.
The ball fell into the path of Nugent just outside the penalty area and this time he made no mistake with a drilled right-footed finish.