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.
Neither side mustered a chance on goal until Scunthorpe defender Michael Nelson headed Michael O'Connor's corner just wide in the 23rd minute.
Scunthorpe broke the deadlock three minutes later. 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.
Home midfielder Mark Duffy then forced Ashdown into two saves in quick succession, the first from a right-footed lob the Pompey keeper did well to parry and then a more routine catch from a thumping drive from outside the penalty area.
O'Connor was next to test Ashdown with a shot from similar distance, but the visiting goalkeeper was equal to it.
Portsmouth's visiting fans had to wait until time added on at the end of the first half for their side's first effort on goal, midfielder Liam Lawrence pulling his fierce 25-yard shot just wide.
Three minutes into the second period Pompey striker Nugent broke away from his marker to head Lawrence's corner straight at Iron goalkeeper Josh Lillis.
Pompey were enjoying their best spell of the match and Hermann Hreidarsson's stinging volley was blocked by Scunthorpe defender Paul Reid.
But Scunthorpe went close to doubling their advantage in the 53rd minute on the counter-attack when O'Connor's drive was well saved by Ashdown.
Portsmouth almost drew level in the 55th minute as the game sprang to life as Nugent's 25-yard shot cannoned back off the post with Lillis well beaten.
Nunez then forced Ashdown into the save of the game with the Honduras international's 35-yard thunderbolt tipped away at full stretch, while at the other end Lawrence's long-range effort was held by Lillis in more routine fashion.
Scunthorpe goalkeeper Lillis was then forced off through injury and his replacement Sam Slocombe was quickly into the action, hurling himself full length to keep out Nugent's curling effort from the edge of the area.
Ashdown denied Iron midfielder Duffy as shots from distance rained in on both goalkeepers, another shot from Lawrence flying over the crossbar.
Portsmouth were then rewarded for another concerted spell of pressure when Nugent pounced in the area to despatch a low finish after the ball rebounded off home defender Nelson.
Ashdown pulled off another fine save soon after to keep his side level, pushing away O'Connor's curling free-kick, while Hreidarsson headed David Cotterill's cross wide of the target.
Pompey pressed for the winner in the closing stages, but Nugent's late shot was blocked by Nelson.