A moment of magic from Sean Raggett looked to be enough to earn all three points for the battling Blues.
But substitute Jonah Ayunga controversially converted in a congested penalty area right at the death to boost the Shrimps’ hopes of beating the drop.
Danny Cowley made three changes from the side that secured a dramatic win over Lincoln on Good Friday.
Ronan Curtis was rewarded for coming off the bench to net the winner, while there were also starts for Ryan Tunnicliffe and Shaun Williams.
Aiden O’Brien and Louis Thompson dropped to the bench and Joe Morrell missed out completely after going off early against the Imps with a dead leg.
Trevor Carson started between the sticks for the home side, who had fellow former Fratton loanee Toumani Diagouraga on the bench.
The visitors started brightly and when Clark Robertson nodded the ball down, Raggett had a shot blocked and Tunnicliffe then fired over.
But it was Morecambe who began to look more threatening and Dylan Connolly bent the ball inches past the post after Cole Stockton’s pass sent him racing away.
Williams tried his luck at the other end of the pitch, but although his effort was cleanly struck, it flew straight into Carson’s arms.
Pompey then had Gavin Bazunu to thank for a series of smart stops that prevented the home side from forging ahead.
He just about got his fingertips to a low Arthur Gnahoua shot to tip the ball against the inside of the post, where it then ricocheted to safety.
And the keeper was at it again moments later to prevent Stockton from turning home a Greg Leigh delivery.
The danger was not over, though, and Bazunu had to recover quickly to save the striker’s follow-up effort with his feet.
It was not until the end of the first half that the Blues began to find a bit of rhythm and pass the ball around with fluidity.
And they made their late pressure count when Robertson lifted a pass into the box and Curtis rose to nod it into the mixer.
The ball fell to the feet of RAGGETT, who brought it under control and spun before hooking a superb shot against the upright and into the net.
Leigh threatened for the hosts once the action restarted, but after doing the hard work to get into a good position, he dragged his effort wide
George Hirst then got forward at the other end and bent an attempt narrowly off target in a lively opening to the half.
But the Blues were almost undone in comical fashion on 54 minutes when there was hesitation over who should deal with a pass through the defence.
Bazunu eventually came out to clear and kicked the ball against Gnahoua, with the ricochet sending it inches past the post.
Ousmane Fane then teed up Stockton with a square pass across the edge of the box, only for the striker to fire straight at Bazunu.
Cowley responded with a couple of changes just past the hour mark, as Williams and Michael Jacobs made way for Thompson and O’Brien.
Pompey were looking for a second goal and Hirst fired a low shot wide after doing well to nab possession on the edge of the box.
A final throw of the dice from Cowley came on 72 minutes, with Mahlon Romeo on for Marcus Harness.
That came after a Bazunu clearance had been charged down by Adam Phillips and the ball flew wide, while the Morecambe midfielder then wastefully shot wide after being found by Stockton.
The hosts stepped up the pressure in search of a late leveller and Diagouraga thought he had found one, only for referee Robert Madley to spot a hand being used as the ball was bundled into the net.
But they were finally able to celebrate deep into stoppage-time when Bazunu came to collect a Leigh corner.
He was unable to hold on amidst a sea of bodies, though, and Ayunga forced the ball home, with Madley ignoring Pompey appeals for what looked to be a foul.
Morecambe (4-1-4-1): Carson; Leigh, Bennett, Bedeau, Gibson; Fane (McCalmont 77); Connolly (Diagouraga 68), Phillips, Wildig (c) (Ayunga 60), Gnahoua; Stockton
Goals: Ayunga 90+3
Subs not used: Smith, Cooney, O’Connor, McLoughlin
Pompey (4-2-3-1): Bazunu; Carter, Raggett, Roberson (c), Ogilvie; Tunnicliffe, Williams (Thompson 63); Harness (Romeo 72), Curtis, Jacobs (O’Brien 64); Hirst
Goals: Raggett 41
Subs not used: Webber, Vincent, Mingi, Walker
Referee: Robert Madley
Attendance: 4,893 (806 Pompey fans)