In a game of real entertainment, the visitors struck first after 17 minutes when David Rodriguez drilled in his first Brighton goal with a near-post effort.
But Blackburn struck twice before the interval when Jordan Rhodes diverted Tom Cairney's free-kick past Tomasz Kuszczak before Cairney marked his first appearance since February with a smart close-range finish.
Gordon Greer flicked in an equaliser with 11 minutes remaining before he was adjudged to have brought down Rhodes, who stroked home his 50th Rovers goal from the spot.
But Bowyer's side were sucker-punched with a fine header from Dale Stephens moments later to extend Rovers' home winless run to four, and the manager showed his displeasure after a result that leaves his side seven points from the play-offs.
He said: "We're on the receiving end of it tonight. In the last two games it's been us scoring late on, but I think that's the least we deserved. Brighton only had four shots on target. I'm majorly disappointed because the first goal we scored was an outstanding finish, second goal was an unbelievable move and third goal was a penalty.
"And then you look at the goals we've conceded, I'm majorly disappointed with the standard of goals.
"We just said there we can't keep saying 'we've scored three goals'. We've scored eight in the last three games and we've got three points to show for it.
"The manner in which we conceded the goals is not acceptable. We've kept 12 clean sheets this season and we have to get back to that quickly because we're scoring goals.
"We've got to turn these performances into results and start winning games instead of drawing games otherwise it's going to cost us."
In the disappointment, Bowyer was quick to praise 'magnificent' Rhodes as his second score brought up his half century of Blackburn goals in just under two seasons.
"Magnificent. In under two years that's some going. The first goal is an outstanding finish and the second goal, he's so cool taking the penalties," Bowyer said.
Blackburn's recent indifferent run has now seen them win just once in the last eight but Bowyer believes with the correct application, the play-offs are still achievable.
He said: "We have to work hard on the training ground and get back to that mentality of not conceding goals, clean out individual errors and piece it all together for a final push."
Brighton missed a chance of their own to put pressure on sixth-placed Reading but the draw moves them within three points of the final play-off spot and ends a run of three straight defeats.
Brighton assistant head coach Nathan Jones was pleased with the character displayed to halt that run.
He said: "Today was the least effective we've been in terms of possession and control of the game and ironically enough we scored more goals than we have in the previous three but that's football.
"We're very pleased with that point because it stops the run we're on, it's a game in hand so it takes us a point closer to the play-off pack so that's one pleasing thing.
"Nowadays if you're four points off it, it takes two results and two games. Now it's one game to get us back in it and that's a positive really.
"Plus the manner of it, to concede a penalty in the 86th/87th minute which we feel was unbelievably harsh and then to come back to get a point, we're pleased.
"We've got a fantastic character. It's just that we haven't had to be in that position too many times this season where we've had to chase stuff after conceding late goals because our defensive record has been outstanding so it shows a lot of character."