Pompey had recovered from a poor start at Oakwell to get themselves back into the contest.
Colby Bishop converted Joe Rafferty’s cross early in the second half to leave the visitors trailing by just a single goal.
But Devante Cole then struck at the other end soon after to quickly extinguish any hopes they had of taking points home to the south coast.
It was a moment that particularly annoyed Sean Raggett and saw the Blues’ winning run come to a close.
Pompey’s skipper said: “It’s really disappointing and we made a few mistakes in the first half that have hurt us.
“We did come out after the break and react to that, getting the goal, but the third one we’ve conceded has killed us off.
"There’s generally a good mood among the group, so we need to make sure that this result is just a blip."
“After managing to drag ourselves back into the game and being in the ascendency, that was so frustrating.
“You come to Barnsley and know it’s going to be tough, so we had to react better to the errors that were made.
“Everyone’s pretty gutted – we had been on a decent run of form and went into the game full of confidence.
“Obviously the dressing room was really down afterwards because we wanted to put in a good performance.
“We’ll keep fighting and will just take things game by game, then see where we are at the end of the season.
“There’s generally a good mood among the group, so we need to make sure that this result is just a blip.”