Rudy Gestede's stoppage-time header snatched a point after Cristian Battocchio looked to have won the game for the Hornets with two minutes remaining.
But the Blackburn boss thought the penalty awarded against Todd Kane for handball that allowed the home side to level at 2-2 was a key point in the match.
He said: "We were comfortable at 2-1 and the penalty changes the course of the game.
"Our lad is stood two yards from (Ikechi) Anya when he crosses it and the ball hits the hand.
"We need to clarify, for the sake of the game, what is handball in the penalty area because you guys, you report on it and one week it's not been given and one week it has been given. We need some clarification because it changed the course of the game."
Watford made the early breakthrough when Marco Cassetti fired home but they were pegged back midway through the first half when David Dunn equalised.
Dunn turned creator to set up Craig Conway to give Rovers the lead in the second half but Troy Deeney's controversial penalty and a late breakaway goal from Battocchio looked to have secured a home win until Gestede's late leveller made it 3-3.
"We were good," said Bowyer. "You look at the quality of our goals tonight, our goals have been excellent.
"The first one's an outstanding finish from Dunny, the second one's fantastic footwork from Dunny and sets Craig Conway up and the third one is an unbelievable header from Rudy, who was unplayable all night. He caused them no end of problems.
"We gifted them the goals.
"The first one we've not marked properly, the second one is a penalty that we've just discussed and the third one is a counter from our free-kick where we should have defended that one better.
"But overall we've come to a team that have won six out of the last six at home without conceding a goal and scored three goals and could have scored more.
"We're making giant strides but we've got to be more ruthless and see the game out."
Hornets head coach Beppe Sannino was left to lament another case of what might have been as his side paid the price for conceding yet another late goal this season.
He said: "I'm very disappointed but in English football you have to pay attention to the last, last minute of the game. This is the rule of English football.
"We nearly won this game but it was not only this game. Since I joined the club there were many games we have dropped points in the last five minutes of games. This game reflects Watford's season perfectly."
Sannino admitted his team had struggled with Blackburn's direct approach, and added: "Tonight I think the Blackburn goalkeeper was the assist man of the game because he was throwing a lot of balls in the box from all positions.
"Their strikers are very physical and they caused a lot of problems with long balls in the box. I knew that Blackburn could cause us problems physically in the box and, in fact, we were struggling in this aspect but I'm disappointed because a football team three minutes until the end should defend differently and to see the match [through to the] finish.
"I'm sure that if we could finish the match 10 minutes before we could be in a very different position and much higher in the table. And this is my big disappointment for the club, the supporters and for my players."