It was just the second league defeat that Pompey have suffered all season.
And Kenny Jackett conceded that his team were simply second best during the first half of their Fratton encounter with Charlton.
Goals from Karlan Grant and Nicky Ajose ensured the Londoners had a commanding lead at the interval.
The hosts did fight back following the restart, but a late effort from Andre Green was all they had to show for it.
Jackett was disappointed that his side took so much time to hit their stride, but also felt their opponents deserved credit.
The Blues boss said: “I thought Charlton were the better team in the first half and we just couldn’t get to grips to them – they had Championship quality on the break.
“We had a good second period and were perhaps unlucky by the end not to have got something out of the game.
"I don’t believe in luck – you make your own. We have to analyse what happened at the start and try not to repeat that."
“It was the reversal of many of our matches this season, where we’ve dominated early and defended after the break.
“We felt that things needed to change in the second half, although there was certainly no lack of effort or application.
“I felt we could get one goal and then have a real go at Charlton, but there were just some things that didn’t go our way.
“Our opponents put their bodies on the line and just rode out those periods when we put a lot of pressure on them.
“We got the crowd going after the break and they were right behind us, but we don’t want to be in situations where we have to come back.
“I don’t believe in luck – you make your own. We have to analyse what happened at the start and try not to repeat that.”
There were several moments of controversy, with Pompey feeling that the ball had gone out of play just before Charlton’s second.
Several penalty appeals were also turned down by referee John Brooks, while Ben Thompson was sent off late on following a challenge with Lyle Taylor.
Jackett said: “The players say it was out of play for the goal, but the fact is that it wasn’t because the officials didn’t give it.
“I think they also felt there was a handball on the line, although it’s not one I’ve looked at it because you can’t do anything if it’s not given.
“The sending off happened right in front of me and I was very surprised when the referee showed a red card.
“It was two committed players who went in equally hard, but fairly. It was a harsh decision in my opinion and it’s one that we will be appealing.”