Pompey Ladies conceded a goal in the third minute of stoppage-time to suffer their first defeat of the season.
Kit Graham struck at the death to ensure that Charlton maintained their 100 per cent record by securing a maximum haul of points at Westleigh Park.
But it looked like it was going to be the Blues’ day when Grace Coombs was sent off for kicking out at Shannon Albuery inside the box early on.
Molly Clark stepped up to take the penalty, only to see her fierce effort well saved by Addicks keeper Katie Startup.
The hosts tried to make the most of their numerical advantage, with Samantha Quayle, Clark and Natasha Stephens all going close before the break.
Clark also saw an audacious effort from 35 yards cannon back off the post, with Albuery’s follow-up attempt saved.
"There were times when we could have circulated the ball with a bit more intensity."
Pompey continued to look the more threatening side in the second half and Startup almost spilled Rachel Panting’s shot into her own net.
Clark then had another chance in the closing stages, but was not quite able to guide Stephens’ teasing cross on target.
And they were made to pay for their profligacy just before the final whistle when Graham pounced on some sloppy defending to score Charlton’s winner.
Blues boss Jay Sadler told the club’s YouTube channel: “There were times when we could have circulated the ball with a bit more intensity and created some more chances.
“Teams like Charlton have got plenty of quality and it could have been either side that nicked it at the death – unfortunately it was them.
“Sometimes it can galvanise teams when they go down to 10. They sat back and we weren’t playing the right passes.
“There was a loss of concentration from a number of people at the end and they punished us for that.
“It’s always difficult to take, but this game is done now and the important thing is how we react to it. We don’t want to feel like that again.”
Pompey: Beazley; Kirby, Soutgate, Widdowson, Bazan (c); Quayle, Clark, Barron (Sievwright 46), Stephens; Panting, Albuery (Hillier 57)
Subs not used: Perkins, Currie, James