The Tykes suffered a 5-1 defeat at Brighton in August, but goals from Jason Scotland and Chris Dagnall helped them avenge that result and boost their survival hopes.
Leonardo Ulloa had levelled for the visitors, but he then missed a late penalty and Flitcroft felt his side deserved a reward for shackling Albion's potent attack.
"I am very proud, we have set a team up to battle and they have done that in the first half," he said.
"I have got massive respect for Brighton on terms of the football they play. I am a massive Brighton fan in terms of that.
"We got schooled down there earlier in the season and that was one of the worst trips I have had.
"But I am delighted because the game plan we set out has worked.
"We didn't let them play with any freedom or fluidity and I don't think any of their players would have enjoyed playing here."
This first win in four Championship games lifted Barnsley out of the drop zone and moved them past the 40-point mark and Flitcroft has challenged his side to continue their charge to safety.
"The main target I set when I came in was to get to 40 points as fast as possible," he said.
"I don't think anyone other manager coming in could have got there as fast, I strongly believe that.
"Now we have got to that and we are going to set another target and kick on again. We have got to win games."