The 26-year-old striker pounced on a loose ball in the area to turn home Pompey's equaliser in the 81st minute after on-loan Leeds winger Ramon Nunez had fired Scunthorpe ahead midway through the first half with a fine curling effort for his third goal in four games.
Scunthorpe's relegation was confirmed last week when they were thrashed 5-1 at Nottingham Forest, but they made every effort to give their supporters a lift on the last day of the season and it took a spirited fightback from Pompey to deny them all three points.
Scunthorpe broke the deadlock in the 27th minute. Nunez cut in from the left channel and curled a fine shot from 20 yards beyond Pompey goalkeeper Jamie Ashdown low inside the far post.
Portsmouth were rewarded for another concerted spell of pressure when Nugent pounced in the area to despatch a low finish after the ball had rebounded off home defender Nelson.