Craig Dawson struck the winner from close range with around half an hour remaining after Tykes goalkeeper Luke Steele fumbled Marcos Alonso's free-kick.
Wanderers had been in complete control at half-time thanks to David Ngog's finish at the second attempt and a deflected drive from Jay Spearing, but Tomasz Cywka and Chris O'Grady brought the hosts level within eight minutes of the restart in an entertaining game at Oakwell.
"I don't really do interesting games, I do wins," Flitcroft said. "We've got to win football matches and we didn't do enough first half to win that football match.
"We waited, we delayed, we were on our back foot and to win a football match, to win a fight, you've got to be on your front foot. You've got to be throwing the punches, instead of taking them and first half we took too many punches.
"Second half: front foot, fighting, we showed guile, we showed bravery and we took a Bolton team on that couldn't cope with that dominance and we've only dominated them for 45 minutes. We haven't dominated them for the first half, which is disappointing."