Morecambe goalkeeper Barry Roche headed home a last-gasp leveller to cruelly deny Pompey victory at a gusty Globe Arena.
The Blues were seconds away from brushing off their FA Cup disappointment by returning to winning ways in the league.
Gareth Evans struck late in the first half and it looked like it would be enough to secure all three points in a game of few chances.
But Roche came up for a corner in the final minute of stoppage-time to grab an unlikely equaliser.
Paul Cook made four changes from the outfit that were narrowly beaten by Bournemouth at the weekend.
Deadline day loan signing Michael Smith was thrown straight into a side that was set-up in a more traditional 4-4-2 formation.
Winger Kal Naismith was a surprise inclusion, making his first Pompey appearance for almost three months.
There were also starts for Adam Webster and Evans, as Christian Burgess, Gary Roberts, Kyle Bennett and Adam McGurk all dropped to the bench.
The visitors made a bright start and Andy Parrish was well-placed to clear Marc McNulty’s low cross before it could reach a blue-shirted player.
Evans then stole possession in a dangerous position, but could not quite thread a pass through to McNulty.
Webster was grateful to Ryan Fulton at the other end on 13 minutes after his sliced clearance was claimed by the teenage keeper.
But Pompey were soon back on the attack and Smith could not get enough power on his shot to trouble Roche after collecting Enda Stevens’ free-kick and turning sharply in the box.
The Morecambe keeper then almost gave Morecambe the lead in farcical fashion when his goal-kick caught a strong gust of wind.
A back-pedalling Fulton just about managed to grab the ball under his crossbar and had to palm it away to stop his momentum taking it over the line.
The conditions were making life difficult for both sides, with the gusts and bobbly pitch not exactly conducive for the Blues’ usual passing game.
But they almost forged ahead on 28 minutes when Webster met Naismith’s corner and saw his angled volley cleared from the line by Kevin Ellison.
Debutant Smith then went close with a curling effort that was deflected narrowly past the post.
The wind aside, Fulton was not being overly troubled and a long-range strike from Tom Barkhuizen flew straight into his arms.
Pompey were looking more threatening, however, and the hardy bunch of travelling fans soon had something to celebrate.
Their side might have taken the lead on 39 minutes, but McNulty blazed over after being sent through by Ben Close.
They only had to wait a few more seconds for a goal, however, as Naismith did well to tee-up EVANS for a cool finish.
Smith tried to add another before the break, but his fierce effort from distance fizzed narrowly past the post.
Half Time: Morecambe 0 Pompey 1
Pompey continued to look the more dangerous side once the second half started and soon had a couple of openings.
First McNulty burst into the box, only to see his low centre cut out by Parrish before it could reach a team-mate.
And the wind was then playing its old tricks when Close’s corner landed on the crossbar and was bundled away by Roche.
The Blues kept up the pressure and Naismith’s free-kick clipped the top of the wall after Andrew Fleming had been booked for handling just outside the box.
Morecambe were not doing enough to threaten the visitors’ lead, but Luke Conlan finally found space down the left 70 minutes, only for his low cross to evade everyone on its way out of play.
Cook made a double switch moments later, with Naismith and Smith making way for Bennett and Roberts.
But the tide was starting to turn in the Shrimps’ favour and they were forcing their opponents into some sloppy passing.
And the hosts were not too far away from an equaliser on 81 minutes when Jamie Devitt curled a shot onto the roof of the net.
McGurk came on for McNulty for the closing stages as Cook decided to freshen up his forward line.
Pompey looked to have hung on for the win when Fulton flung himself to the left and kept out Lee Molyneux’s strike in the fourth minute of stoppage-time.
But there was still time for Roche to rush forward for the resulting corner and grab a point for Morecambe.
Morecambe (4-2-3-1): Roche; Beeley (c), Dugdale, Parrish, Conlan; Goodall, Fleming; Barkhuizen, Devitt (Molyneux 82), Ellison (Mullin 75); Miller
Goals: Roche 90+4
Booked: Fleming, Beeley
Subs not used: O’Hara, Edwards, Wilson, Doyle
Pompey (4-4-2): Fulton; Davies, Webster, Clarke, Stevens; Evans, Close, Doyle (c), Naismith (Bennett 72); Smith (Roberts 72), McNulty (McGurk 83)
Goals: Evans 40
Subs not used: Bass, Burgess, Barton, Chaplin
Referee: Richard Clark
Attendance: 1,399 (479 Pompey fans)