Substitute Bobby Hassell scored the only goal of the game 15 minutes before the break.
The long-serving Tykes defender, a seventh-minute replacement for the injured Rory Delap, rose highest at the back post to head in Jacob Mellis' left-wing free-kick for his first league goal in more than two years, and Flitcroft said: "I'm completely buzzing, we set out a game plan and it really worked.
"There's been a lot said about Watford and what they've tried to do and how they've done things. I think it's brilliant what they've done; I love creativity, I love the way that they've taken advantage of a situation. You've got to accept you're playing Watford, you're playing some top, top players and you've got to deal with them; we dealt with them.
"At the start of the season we got overrun by them and (here) we've got up close and personal. We've got in and around what they do, we've put them under real pressure and we've returned with three points and victorious, and it's an honour to manage this football team at this point.
"I don't know many times Watford have not scored (this season), and I'm going to look that up when I get back to the office. We've kept a clean sheet against Watford, this can't be underestimated; the size of this performance, the level, the hunger, the desire that I spoke about before the game, it was just evident."
Watford manager Gianfranco Zola said his players will learn from the loss as the high-flying Hornets dropped more points in the promotion race with a second successive defeat.
Zola said: "I'm disappointed for the result, I'm disappointed for the performance and that's it.
"But it ends there because sometimes you have to admit, when the opposition fights and plays the way they played, sometimes the better quality doesn't prevail - especially in the Championship when you have teams fighting for their lives, like Barnsley, and they make it difficult for you to play and you cannot overcome that.
"I think my players will learn a lot. For many of them, they didn't even know a game like this. It is the first time we have faced a team that has played and pressed us so much throughout the game. And as I said, many of them with learn. In my team I have a lot of young players and games like this will teach them a lot."