First-half efforts from Tom Naylor and Gareth Evans fired the Blues further clear at the summit, as second-placed Sunderland were held to a 2-2 draw against Walsall.
Lee Novak pulled on back for the Iron on the hour and Pompey were holding on towards the end.
But Kenny Jackett's men saw it out, clinching a first-ever victory at Glanford Park in the process.
It was a lively opening and the Blues should have gone ahead after 11 minutes.
Evans'Â fizzed corner found centre-half Matt Clarke but his glancing header went just wide.
Pompey continued to probe, having a penalty appeal waved away four minutes later.
Oli Hawkins went down under a challenge from Cameron Burgess in the area, with referee Martin Coy waving play on.
The home side had fired a couple of warning shots before spurning a great opportunity on 19 minutes.
Welshman George Thomas' corner found Matthew Lund whose header from eight yards out went over.
Having looked the more threatening, the Blues took the lead 11 minutes before the break.
Jack Whatmough fired Republic of Ireland international Ronan Curtis' corner back in to a dangerous area, with Naylor cleverly poking past Jak Alnwick on the spin.
Pompey enjoyed a dominant spell after going ahead, making the pressure count with a second after 40 minutes.
Evans superbly took a pass in his stride before looping a fine strike over Alnwick.
The Blues should have put the game beyond the Iron 13 minutes after the restart, only for Evans to fire over from all of four yards after Naylor's fine delivery fell fortunately at his feet.
Scunthorpe then had a lifeline two minutes later. Craig MacGillivray parried Thomas' cross and frontman Lee Novak crashed home.
Stuart McCall's side were threatening a leveller and nearly had it through Thomas. The Leicester loanee curled agonisingly wide from 20 yards 15 minutes from time.
Pompey were hanging on now, with Iron coming close again. This time Thomas' free-kick flashed across the face of goal, somehow going wide of the far post after 83 minutes.
Despite their dominance in the closing stages, Scunthorpe could not find a leveller and Pompey held on.