Full-time: Portsmouth 2 Scunthorpe United 1
Disappointing defending saw Scunthorpe United's four-match unbeaten run come to an end at League One's crisis club.
Debutant Wes Thomas sunk the Iron with only 60 seconds to play at Fratton Park, earning cash-strapped Portsmouth a priceless first home victory of the season.
Earlier, the heroics of substitute goalkeeper James Severn looked to have earned United a point in one of their longest trips of the campaign.
The 20-year-old, on as a first-half substitute for the injured Sam Slocombe, brilliantly beat away a 30th minute from penalty from Brian Howard.
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The spot kick stop followed a fifth goal in as many games for on-loan striker Leon Clarke that had put Scunthorpe in front early on, though the hosts levelled six minutes after the deadlock was broken when Gabor Gyepes lashed in following more slack play at the back.
United had chances to bag a potentially decisive second goal, but failed to score twice in a match for their 15th successive league outing.
Scunthorpe – chasing a first win at Fratton Park since 1964 – had club captain Paul Reid in their matchday squad for the first-time this season following his hand injury.
But the centre-half had to be content with a place on the bench as manager Alan Knill named an unchanged starting line-up for the third match in succession.
As had been the case in a couple of other games in their unbeaten run, Scunthorpe wasted no time in getting on the front foot.
Good build-up play down the left hand side saw the ball worked into the area for Jimmy Ryan and he cleverly threaded a pass inside from which Clarke thumped the ball into the bottom corner in only the sixth minute.
Questions had been asked of Pompey's fragile confidence in the build-up to this clash, but with a vocal crowd rallying behind them, despite such an early setback, they came out firing.
The Iron had already survived a couple of hairy moments when Gyepes thundered them back on level terms in the 12th minute following a corner that had not been cleared.
Skipper Howard swung the flag kick into the box, Lubo Michalik powered a header goalwards which Slocombe clawed away at full stretch, but the ball fell invitingly to first Izale McLeod, who swung only at thin air, and then the Hungarian centre-back, who spared his team-mate's blushes.
The equaliser signalled the start of a period of play in which Pompey had long spells of possession, but United – and in particular Clarke – looked dangerous on the break.
Darel Russell chipped Slocombe, and the visiting goal, after latching on to Lee Williamson's perfectly-weighted pass from out wide, while at the other end, Hawley tested Portsmouth keeper Mikkel Andersen with his left foot after Clarke had nodded a deep cross down into his path.
Less than five minutes after his introduction, with Slocombe forced off by a deadleg sustained in the build-up to Portsmouth's goal, Severn was beaten by a brilliant curling shot from McLeod that was packed with power and pace.
But fortunately for the Iron's replacement stopper, the effort smacked the face of the bar before bouncing clear.
Although unable to do anything about that effort, the same could not be said about the penalty which kept the Iron score 1-1.
Howard stepped up confidently after Tom Newey was adjudged to have tripped Thomas right on the edge of the visiting penalty area, but the former Derby County stopper dived to his left and pushed away the midfielder's strike.
The second half didn't flow as fluently as the first, but still both sides created openings.
Scunthorpe threatened quickly after the restart as Hawley's square ball found Clarke and the in-form front man lifted a left-footed shot only inches wide of the target from inside the D.
So too, though, did Portsmouth - with the Iron's defending gradually becoming more stretched.
In the 62nd minute Thomas, brought in on loan from Bournemouth in the build up to this match, and Howard both slid in to meet a dangerous delivery from Mustapha Dumbuya, but only succeeded in putting each other off as the ball flew over the bar.
A mazy run from substitute Ashley Harris – whose introduction made the hosts much more of threat down the left flank – took Pompey closer, though he still could not hit the target.
Scunthorpe tried to interject a bit more into their wide play by bringing on former Sheffield Wednesday and Rotherham winger Chris Sedgewick, but he could not wrestle the contest back the visitors' favour.
Instead it was Pompey who continued to look the likelier scorers, with the pace of Thomas and McLeod causing United problems as the match entered the final quarter.
Severn rescued Scunthorpe with three minutes to go, denying Dumbuya after Lee Williamson had cut Scunthorpe open when running in from the right.
But the Iron keeper was rooted to his line in the closing stages as his side again failed to stop the ball entering their box from the right and when David Prutton failed to clear, Thomas stole in to force home Portsmouth's winner.
PORTSMOUTH: Andersen, Webster, Gyepes, Michalik, Harley (Harris 58), Dumbuya, Russell (Ertl 67), Howard, Williamson, Thomas (Obita 90) McLeod. Subs not used: Eastwood, Walker, Compton.
SCUNTHORPE: Slocombe (Severn 24), Ribeiro (Grella 90), Mirfin, Canavan, Newey, Duffy (Sedgewick 76), Walker, Prutton, Ryan, Hawley, Clarke. Subs not used: Reid, Barcham, Jennings, Gibbons.