Christian Saydee’s second-half goal cancelled out Peterborough’s David Ajiboye’s opener as the match finished 1-1 and headed straight into a shoot-out.
After Ryan Schofield saved Ryan De Havilland’s penalty, Abu Kamara had the chance to win it, only to sky his effort into the Milton End.
Then, in sudden death, Joe Morrell struck a post, with Ajiboye stepping up to claim a 5-4 victory.
But Mousinho was not blaming Kamara and Morrell for a first loss in 19 matches in all competitions.
Pompey’s head coach told The News: ‘I have no problem with that, I’ve been in those situations, it’s really difficult.
‘You have to show a lot of steel to step up and take penalties in these situations, it’s never easy, there’s a lot of pressure and I have nothing but respect for the lads that did step up and take them.
‘No problem whatsoever with missing the penalties, the issues I have are during the game rather than anything which happened after it.
‘Particularly in the first half when I didn’t think we were particularly front-footed, we waited for things to happen and waited to go 1-0 down.
‘We had to come in at half-time and have a real stern word about what we needed to do differently – and it was completely different in the second half.’
Peterborough had to see out the final 31 minutes with 10 men following Charlie O’Connell’s sending off.
At the time the scoreline was 1-1 – and that is how it remained with the Blues unable to find any way through despite dominating.
Mousinho added: ‘In the first half I was really displeased in the way we went about our business in terms of the press.
‘We weren’t quite aggressive enough, we didn’t move the ball quickly enough, we weren't positive enough when we did get it and it was chalk and cheese in the second half.
‘After the break I thought we were excellent, we came out on the front foot, much more aggressive, 10 yards higher up the pitch, and got our rewards in scoring the goal and the game changed when the man got sent off.
‘I was really, really pleased with the performance in the second half, we got ourselves into a position to win the game, but it wasn't to be.’