Ryan Williams and Ronan Curtis failed to convert their spot-kick at Wembley to deny the Blues back-to-back Trophy wins.
It was what Richie Wellens’ side deserved as Kenny Jackett’s side were indebted to Craig MacGillivray for taking the match beyond extra-time with a phenomenal display.
Without the Scot, Pompey would’ve have been comprehensively beaten as Salford carved out a stack of chances and pummelled their opposition in the first half.
It was better after the break for Jackett’s side, but they could have no complaints at the outcome with a result which puts another dent in their season.
The first 45 minutes were frankly embarrassing for Pompey.
Salford created chance after and chance and could have easily been out of sight by the interval.
Craig MacGillivay thumped away James Wilson’s 25 yarder after seven minutes, before Ibou Touray couldn’t connect with a cross at the far post three minutes later.
Charlie Daniels was having a shocker and gifted Brandon Thomas-Asante the ball after 15 minutes, but MacGillivray again palmed away his drive.
MacGillivray once more denied Wilson in the 27th minute with a great close-range stop after Touray’s cross.
A number of crosses were flashed across Pompey’s box towards the end of the half with the Blues failing to register a single shot at goal.
There were unsurprisingly changes at the break with Marcus Harness, Ronan Curtis and Lee Brown on for Daniels, White and Hiwula.
Curtis immediately had a great chance to open the scoring, but Vaclav Hladky produced a smart stop to smother the Irishman’s effort when through on goal.
But it was MacGillivray Pompey were once more indebted to in the 67th minute, following a world-class point-blank stop from Eastham’s header from a couple of yards.
Pompey had a great chance to win it with 10 minutes left but Curtis completely fluffed an acrobatic volley from a sumptuous Ben Close cross. It was a golden opportunity.
Brown was a whisker away from winning it with a volley from 10 yards late on.
Then MacGillivray made yet another world-class display to deny Bruno Andrade at the death of normal time.
That meant 30 minutes of extra-time in which Curtis had an early chance blocked in the box from the lively Close’s cutback.
Pompey had a golden chance to win after 103 minutes when Williams’ effort from 10 yards was kept out by Hladky and Marquis couldn't force home the loose ball.
Then Salford sub Mani Diesuuvwe volleyed a shot on turn inches wide from inside the box.
Williams saw his shot blocked when free in the box with four minutes remaining of extra-time.
The match went to spot-kicks, however, and it was over for Pompey really before it started as Williams fired over the first spot-kick and Curtis saw the second kept out by a fine Hladky stop.
That left it down to former Blackburn defender Jason Lowe to dispatch the decisive penalty to win it for Salford and send Pompey packing.