The former Preston man claimed his seventh goal in eight games against Ipswich before laying on a second for David Cotterill as Pompey took all three npower Championship points.
Ipswich boss Paul Jewell has ignited the club's season since replacing Roy Keane but will be dumbfounded after Steve Cotterill's men took the win.
The hosts dominated the first hour but were made to pay the price for a catalogue of missed chances with teenage prospect Connor Wickham particularly wasteful.
Ipswich were boosted by the return from injury of captain David Norris - a January target for Pompey - but it was the visitors who had the first sighter of the afternoon when a cross from Ritchie De Laet was headed by Dave Kitson straight at Marton Fulop in the Town goal.
A dangerous free-kick from Grant Leadbitter was then headed wide by Damien Delaney as the home side started to take control and they should have had the lead on the quarter hour mark.
Former Sunderland winger Carlos Edwards has been converted to a full-back under Jewell and made the chance after a fine run down the right.
He picked out Wickham at the near post but the teenager saw his stinging volley brilliantly tipped over by Jamie Ashdown.
Wickham then flashed a header across the face of goal after good work from Lee Martin before the visitors ended the half with a chance when Joel Ward headed straight at Fulop.
There was still time for the hosts to miss chances before half-time as Jason Scotland toed an effort into the side-netting before Wickham made a mess of his header to miss from close range.
The 17-year-old was in the thick of it and forced Ashdown into another save after just 25 seconds of the second half, but the goalkeeper was again equal to his stooping header.
Ashdown then repelled a shot from Scotland on the turn as the hosts continued to dominate before Pompey took the lead totally against the run of play in the 55th minute.
David Cotterill sent in a free-kick from the right which found its way to Nugent 15 yards out.
The former England man beat Norris with a touch inside before lashing a drive into the roof of the net to continue his fine record against the Tractor Boys.
Jewell looked understandably perplexed and introduced wingers Andy Drury and Luciano Civelli in a bid to find an equaliser.
But the attacking change backfired as Pompey broke to steal a second goal in the 77th minute.
Nugent was again instrumental with a strong run up the left flank before he cleverly found David Cotterill breaking into the area and the winger calmly chipped the ball over the onrushing Fulop to double the lead.
Ipswich 0-2 Portsmouth: Match Report - view commentary, squad, and statictics of the game as it happened.