Jason Scotland's late strike secured another vital three points and Barnsley have now taken 13 points out of 15 since Flitcroft took over from Keith Hill as manager.
In a fiercely contested match Jim O'Brien gave the visitors the lead in the 25th minute only for Tom Ince to level things after the break.
The sending off of Blackpool goalkeeper Matt Gilks was the turning point before Scotland popped up with a dramatic winner two minutes from time.
"I'll remember those 14 players who turned out today for the rest of my life," said Flitcroft, who signed Scotland following his release from Ipswich earlier this month.
"There was bravery out there from start to finish - we just showed no fear whatsoever.
"The (Blackpool boss) Steve Thompson way is very much a mirror image of the Ian Holloway at Blackpool so we didn't underestimate how tough it was going to be.
"They get players into some incredible positions, but for all that we've matched them and we really had to dig deep in every way.
"Every single player on the field played a major part and we've proved again that there's no room for complacency at this stage of the season.
"It was probably the hardest game of the season, but the lads have dug in and got the result. I've not set any targets yet, that's not really my style, we just have to worry about ourselves.
"We've just got to continue concentrating on what we do and now worrying about others. If we carry that on we'll get out of trouble."