The hosts convincingly outplayed and outworked his team, and had the Saints even been slightly more clinical in the final third they would have won by a far greater margin than that provided by goals from Shane Long and Dusan Tadic.
Watford were sluggish throughout and occasionally erratic, but having inspired his team to an impressive first half of the season, in which they have often appeared capable of challenging for European football, their manager was reluctant to be negative.
"I'm not angry, I'm disappointed, but not angry," Flores said.
"We have the feeling we didn't play in the right way
We made mistakes, we made Southampton's play very easy
They played much better than us.
"But it's the first time during the season we've had this feeling, so more than ever supporting the players, transmitting to the players it's possible to make mistakes..
it's the first time, we need to understand sometimes it's possible.
"It's the first time we feel that we were not competitive
It's the first time the opponent is much better than us
I apologise to the fans
My feeling is to give more support than ever to the players, it's the first time in six months we've had this feeling
We can learn for the future.
"It's football, sometimes it happens
It's not our idea when we're training, it's not our idea when we are playing the match, it's not the spirit of the team
"Our spirit is very high, it's very positive, it's very energetic, but we didn't find this spirit, and Southampton played really well."
Southampton's impressive performance was a welcome return to form for Ronald Koeman's men after they had lost eight of their previous 10 games.
The Saints convinced by maintaining an intense work-rate throughout but were profligate with their finishing, though Koeman insisted he was always confident his side would win.
The Dutchman said: "I was not so nervous because from the start we dominated the game, controlled the game
We were dangerous, we created chances
"I prefer to play with three at the back against two strikers
That gives more ball possession
Defensive-wise it's a little bit more sureness, because one of our qualities is our left and right-backs are very offensive players
"We had very good pressing
Oriol (Romeu) and (Jordy) Clasie were very good in the midfield
"We can (start to) look up (the Premier League), but we also have to look under us, because it's close.
"(Watford) are doing a great season
They are difficult to beat
Maybe Southampton is one of the teams who created a lot of opportunities, because normally it's not so easy to create opportunities to score against Watford."
Source : PA
Source: PA