Pompey boss Andy Awford cursed the nightmare start which put Tranmere on the road to victory after just 80 seconds.
Shamir Fenelon took advantage of poor defending to score from Max Power’s right-wing corner at the far post.
His goal gave the relegation-threatened hosts the lead.
The Blues didn’t get going in their response until the second half.
But after Jed Wallace levelled, Micky Adams’ side kicked on again with two more goals to ensure a 3-1 victory.
And Awford was left ruing the wretched opening.
He said: ‘It’s alright talking in the dressing room and saying “Let’s do it” but when you go out and defend a set-piece like that it is really frustrating.
‘It’s not just that, we actually cleared the first one – then gift them another corner.
‘We were not professional enough.
‘And the game management wasn’t good enough in the opening two minutes of the game, it’s as simple as that.
‘They got a lift straight away.
‘I mentioned to Paul Hardyman after 25 minutes about them applauding when one of their players kicked it out of play, that was because they were 1-0 up.
‘If it’s 0-0 with a struggling side they don’t applaud.
‘It gave the whole place a lift and we were laboured.
‘But we got in at half-time 1-0. We stayed in the game.
‘We sorted a few things out, improved after the break, got the goal and looked the only team that was going to go on and win it.
‘Then they scored another two to win it.’