Pompey were cruising towards victory with a dominant first half display at Southend.
Bryn Morris, Ben Close and Oli Hawkins were all on target, while Omar Bogle had another effort questionably ruled out for offside.
But Simon Cox grabbed a lifeline for the hosts before the break and went on to complete his hat-trick after it.
And Kenny Jackett knows that his side should have held on for the victory after storming into such a commanding lead.
The Blues boss said: “It’s obviously very disappointing because we were three goals up and in control – we should have seen it out.
“We’ve given a really sloppy one away just before half-time when Cox managed to get the wrong side of Clarke.
"We have to be tough enough to go again and realise the position that we’re in."
“Then after the break we’ve had a really big chance go get a fourth when Omar was sent through on goal.
“But we’ve bundled their forward down unnecessarily for the penalty and Southend’s equaliser was from a bit of quality.
“We’ve lost a few defensive players, with Thompson, Whatmough and Naylor all out. They’re the type who could have helped us to see the game out.
“Now we have to be tough enough to go again and realise the position that we’re in. We’ll be okay for next week because, in football, that’s what you have to do.”
Pompey have mostly used a 4-2-3-1 system this season, but Jackett opted to switch to 4-4-2 at Roots Hall.
He said: “I felt it was the right decision for this game because we’ve got some good options going forward, and I wanted to look at Bogle and Hawkins up front.
“Omar’s just getting cramp in his calves in the second period of games, but I thought it was a positive partnership.”
Pompey were without Nathan Thompson against Southend, with the right-back set for a short spell on the sidelines.
Jackett explained: “He’s got a knee injury that he sustained in training on Thursday and it will keep him out for maybe two weeks.
“Ronan Curtis has been struggling with the flu, but on the plus side I thought that Viv Solomon-Otabor had a decent debut.”