The Fratton Park crowd were waiting for the lottery of penalties to decide the Carabao Cup contest.
Instead, Anton Walkes diverted Tom Soares’ cross into his own net to ensure it was AFC Wimbledon who reached the second round.
That came after Christian Burgess’ header early in the second half had been cancelled out by Joe Pigott.
And Kenny Jackett was disappointed that his side did not build momentum from taking their lead following a lacklustre opening 45 minutes.
The Blues boss said: “We got the breakthrough and it’s the third match on the trot that we’ve managed to find the first goal.
“That’s encouraging and then from that point I was really looking for us to try to take the game on and maybe win it well.
“It didn’t happen that way and Wimbledon scored a good equaliser, while the ending was a real sucker punch.
“An own-goal on 88 minutes didn’t really give us any time to react and I feel for Anton. He’s a young player and he has to get over it.
"Wimbledon scored a good equaliser, while the ending was a real sucker punch."
“At any other time he would be able to head it out of our box, but it seemed to come at him too quickly and he wasn’t able to assess it.
“We couldn’t respond when it looked like the tie was heading for penalties, as many of the games in these early rounds do.
“In the first half we didn’t get things right, but we managed to come through it and finished well before the break.
“Wimbledon kept the pressure on during the game and did manage to play through us too easily in the middle.”
Jackett does not want to dwell on the defeat too much with a hectic schedule of fixtures coming up for Pompey.
He said: “Now we go Saturday, Tuesday, Saturday and have three big games against Oxford, Bristol Rovers and Doncaster.
“Everybody has to be ready and we need to look to bounce back from what’s a disappointing result for us.”