The Clarets' under-23 side suffered a third successive away defeat against a strong Watford side including former West Ham and QPR striker Mauro Zarate and ex-Sporting Lisbon midfielder Marvin Zeegelar.
Michael Duff's side led early on through Khius Metz (above) before Zarate set up a Watford comeback and a 3-1 half-time lead to lay the foundations for their third win in four games in the Professional Development League.
But a youthful Clarets' side again competed well for long periods, leaving Duff frustrated they had nothing to show for their efforts.
The Development Squad coach said: "It's a difficult one really, because its a results' industry.
"Our performance was very good. I think they had five shots on goal and they have scored four of them.
"We totally dominated the game for the best part of 70 minutes, but it is something the players need to learn from.
"They can't keep playing well and getting beat. There are lots of positives to take, but we need to be stronger mentality and we can't give away goals like we did."
It was the Clarets who belied their relative lack of experience and looked sharp early on as Tinashe Chakwana curled an effort towards the far corner, forcing Nathan Gartside into a good stop.
And with 12 minutes gone Duff's men did take the lead as Mark Howarth's free-kick was met at the back post by Flowers.
His effort on goal was blocked by Gartside but the ball fell into the path of Metz, who poked home his second goal in two games.
Burnley nearly had a second not long after as Flowers again rose highest at the far post, this time his towering header floating just wide.
But Watford made it 1-1 just after the half-hour mark when ex-Lazio marksman Zarate picked up the ball just outside the area before curling the ball past Aidan Stone into the top corner as the Argentinian continued his comeback from injury.
The hosts then added their second two minutes before half-time as Jerome Sinclair broke into the penalty area and was brought down by Flowers, the former Liverpool youngster picking himself up to slam home the spot-kick and give Watford the advantage.
And 60 seconds later later the Hornets had a third to lead 3-1 at the break as Michael Folivi collected the ball in the area before rounding Stone and slotting into an empty goal.
The Clarets looked much brighter in the second half and had several chances to reduce the deficit before Flowers met Howarth's corner at the far post 13 minutes from the end, the defender glancing the ball past Gartside to set up a nervy finish for the home side.
But despite Burnley's best efforts to force an equaliser, it was Watford who had the last say as second-half substitute Periera slotted home past Stone in stoppage time to seal the victory.
Burnley: Stone, Birch, Flowers, Wilson, Koiki, Chakwana, Howarth, Nabi, Bayode, Metz (Limb 66) Thomas (McNeil 83). Substitutes: Bruce, N'Guessan, Younger.
Watford: Gartside, Mukena, Rowan, Mason, Eleftheriou, Charles, Stewart, Zeegalaar (Sesay, 70), Zárate (Pereira, 83), Sinclair, Folivi (Bradbury 83). Substitutes: Lacy, Williams.