Bowyer's side took the lead inside the opening minute, but a brace from Jamie Ward and a smart finish from Will Hughes turned the game.
Rudy Gestede pulled one back for Blackburn Rovers but Derby County held on for the win.
"I think a draw was the least we deserved. Lee Grant has pulled off numerous saves, he and Richard Keogh were their best players," Bowyer told Radio Rovers.
"We had a right good go, we were camped in their half, put many balls in the box. We ended with five up front, we ran them really close.
"Obviously we are disappointed with the third goal we conceded because it was a foul all day long on Craig Conway. Everyone knows its a foul, but after that we should have defended it better that is for sure."
The result lifts Derby County up to seventh, while Blackburn Rovers fall to 13th in the Championship table.