It was a game too far for Pompey and their injury-racked squad.
Frustratingly for Paul Cook, the ambition had inevitably switched to a penalty shoot-out as his team limped towards 90 minutes.
Gareth Evans and Danny Hollands had already been sidelined during the opening 45 minutes to decimate the manager’s tactical options.
There were also injury concerns over Michael Doyle, Ben Davies, Marc McNulty, Enda Stevens, Adam Barton and Kyle Bennett.
Even Conor Chaplin, the third substitute to be employed, was carrying a knock.
And Cook admitted he could only watch helplessly as Plymouth booked their Wembley play-off place at the Blues’ expense during a heartbreaking finale.
He said: ‘I am not making excuses, these are facts.
‘We had Conor Chaplin on the bench and he should never have been near a bench in a million years, never.
‘His heart is as big as his body because he wants it that bad.
‘Unfortunately on Sunday night we were on our knees due to other bits and pieces, there was nothing we could do about that.
‘We weren’t hurting Plymouth in the second half, we were hanging on and we don’t do that as a team.
‘Even when we lost at Barnet, we didn’t lose hanging on, we lost because we couldn’t score.
‘That was the disappointing thing for me, I couldn’t help them – and that really upset me.
‘Credit to Hollands. Stevens and Barton for starting, they nearly didn’t make it. For McNulty and Bennett to finish the game showed great courage.
‘Then there were the Hollands and Evans challenges. They would never have made Wembley if we had got there, they are both really nasty injuries and could be out for a long time.
‘We were sitting suffering, with mismatches from set-pieces – Stevens picking Peter Hartley up, Adam McGurk having to pick Curtis Nelson up. We all knew the goal would be from a set-piece.
‘Kyle had trained with us for one day, played 60 minutes in the first leg and couldn’t train again.
‘We couldn’t train on Saturday because we had no players, we had to call training off at Fratton Park.
‘Our lads gave this club everything they had, every single one of them can be proud of what they did on Sunday. Unfortunately they fell short.’
Peter Hartley’s scrappy stoppage-time goal condemned Pompey to a fourth successive season in League Two.
An outcome which hinged on game 48 of the league campaign.
Cook added: ‘I think Plymouth smelt we were labouring, you never usually see us telling our goalkeeper to take his time, we normally wave our full-backs forward.
‘For the first time as a manager I wanted to get to penalties because it would help us.
‘The only positive substitutions we could make would have meant all of our back four going into extra-time, yet we needed more at both ends of the pitch.
‘Sometimes it’s not meant to be.’