Pompey’s energy reserves were depleted following back-to-back home wins over Rotherham and Lincoln.
Their third match in under a week then saw a mammoth trip to Morecambe, who are battling to beat the drop.
But it looked like three points would be heading back to the south coast following a fine first half finish from Sean Raggett.
Deep into stoppage-time, however, substitute Jonah Ayunga bundled the ball home to break Pompey hearts.
And Danny Cowley was fuming after referee Robert Madley missed what he felt was a clear foul on goalkeeper Gavin Bazunu.
The Blues boss said: “We’re really frustrated and angry because we’d emptied the tank and got right the way to the final moments.
“It would have been a well earned away win and then the referee misses three fouls that lead to their goal.
“I’ve watched it back and it’s clear – it’s unacceptable that he’s missed that because it’s right in front of him.
“I rarely moan about the officials, but decisions don’t get more key than that and it’s had a huge impact.
"I’ve watched it back and it’s clear – it’s unacceptable that he’s missed that because it’s right in front of him."
“The referee said he didn’t think it was a foul, but Gavin was in the air and about to catch the ball when there’s a clear two-handed push.
“It was just so obvious and blatant and it’s something that the referee hasn’t got right, which we have to suffer.
“I just feel sorry for our supporters who have travelled the length of the country to get behind us and we just want some consistency.”
Cowley was pleased with the efforts of his side in Lancashire at the end of what has been a punishing Easter schedule.
He said: “We were a team that looked like we’d played three games in six days and the lads gave everything they had.
“Sean scored a great goal after a diagonal ball from Clark Robertson, a good win from Ronan Curtis and then a nice finish.
“It was clear that we were running on empty, but I thought we’d done enough to get over the line to get another three points.”
Joe Morrell made the trip north, although he was not involved in the matchday squad after going off with a dead leg against Lincoln on Friday.
Cowley said: “He wanted to give himself every chance of playing and did a fitness test in the morning, but it was clear he wasn’t going to make it.”