In a repeat of last season's scoreline at Ewood Park, Jordan Rhodes once again scored the crucial goal to give all Rovers all three points against the high-flying Hornets.
To a man the team worked tirelessly throughout and were full value for the win at the end of the game.
"That was a massive effort off the back of the performance we gave at the weekend against Bournemouth," Bowyer told Radio Rovers.
"I have nothing but praise for the energy showed by the players tonight.
"Watford nearly got promoted last season and in my opinion will be there or thereabouts.
"Hopefully now it will give us the belief that we can compete against the so-called bigger teams.
"You can't single anyone out because it was a massive effort from everyone.
"I think the first half was a typical game after a weekend from both sides, not many chances.
"We felt we might have had a penalty with Jordan Rhodes getting sandwiched in between two of theirs, then there was a offside decision where he was clean onside.
"We said to the boys to go and give us everything in the second half and they did. You cannot do anything but give them praise."
Against Bournemouth on Saturday it was Rovers on a roll, whereas it was in the second period on Tuesday night where they really hit their stride.
"When you get to half-time and you are 0-0 against the league's top goalscorers it gave the boys some belief and I think they grew in confidence.
"Almunia has made two very good saves from King and Jordan, so we are delighted with how we have gone about it tonight."
Rovers are back in action this Sunday when they take on Wigan Athletic at the DW Stadium.
Tickets are on open sale priced at £20 Adults, £15 Seniors and 16-21 year-olds, and £10 for Under-16s. Book online today at www.onerovers.co.uk