Ibrahim Diabate's goal on the stroke of half-time proved the difference, and Alavés kept a clean sheet for the first time in 20 matches. It was the club's first league victory over Barcelona since 2001.
Flores, who took charge of a side already deep in trouble when he arrived in Vitoria, reflected on a tactical plan that had been weeks in the making.
"We live in that permanent pressure. When we arrived in Vitoria the team was already in a fairly extreme situation with very little margin for error. Against Athletic and against Elche we had the chance to do something similar to tonight because we went ahead on the scoreboard, but we didn't close the games and let important opportunities to move up the table slip. Tonight we did it and we kept a clean sheet. There is a lot of good news, but we are already thinking about the next game."
On the tactical adjustments that eventually shut Barcelona out entirely.
"In the second half we reached the opposition area less and that prevented us from pressing in pairs at the start of Barcelona's build-up play. In the first half we moved from a 5-3-2 to a 5-4-1 and after the break we understood it better because we closed interior spaces. We managed to generate very few goalscoring chances for them and they finished without a shot on target."
He reserved special praise for winger Abde Rebbach, who was active throughout and caused Jules Koundé problems on the right flank.
"He is a boy who can play as a wing-back because he interprets it very well. He becomes a winger when we attack and defensively he understands very well when he has to press and when he has to tuck behind the centre-back. He is a very interesting type of player, with footballing intelligence and who gives us a lot of pace."
Flores paid tribute to the Mendizorroza crowd, whose atmosphere he identified as a genuine factor in the result.
"The fans were extraordinary once again. They understood the difficulty of the game and the moments. They supported us and created a very hostile environment when Barcelona had the ball. We send them a huge embrace and we are going to need them between now and the end of the season."
On the broader survival picture, he kept the tone grounded.
"We are in that situation of facing games that have no way back. You have to finish matches with the feeling of having given everything. We have played two games against Elche and Barcelona, teams with a lot of possession, and we have made very intelligent readings of the games. The players have been very committed to defending every metre of the pitch. That commitment and the way we read matches gives us the possibility of being closer to the results we want."
Alavés now travel to Mallorca on Sunday before hosting Sevilla on the final day.