The Tykes are bottom of the table and have now lost all six of their away league matches this season.
They defended resolutely before substitute Junior Hoilett tricked his way towards the left-hand touchline and pulled the ball back for Charlie Austin, who netted from seven yards out.
And Austin sealed the win with five minutes remaining when he slotted home from the penalty spot after being tripped by Martin Cranie - the striker's fifth goal in as many matches.
Flitcroft said: "It was probably 20 or 30 seconds of us not doing what we wanted to do which cost us.
"You can't give Charlie Austin two inches. We said before the game that we'd have to mark him because he's a unique goalscorer at this level. Then Martin [Cranie] doesn't have to tackle him there.
"We defended well as a team and limited them to two chances in the first half. We kept them at bay and kept their fans low, but that first goal really gave them energy and verve.
"There were a few tired performances in the last 20 minutes. We just ran out of legs.
"We've got to balance and shape this squad and find out who we're going forward with. It's two weeks to assess things.
"We've got a plan to win football matches and we intend to have a really positive bounce-back after the international break."