Bowyer, who became permanent boss at Ewood Park over the summer after two spells as caretaker last season, watched on as goals from Theo Robinson and James Husband gave Paul Dickov's men the points at the Keepmoat Stadium.
However, he had issues with both efforts, claiming Robinson's first-half header was offside and branding Husband's second-half cross-shot a "fluke".
The defeat, a second in a row after losing to Forest last weekend, might just leave him looking over his shoulder given Blackburn's trigger-happy past where they sacked three managers last season, but Bowyer is convinced things will come good.
"I think we played well with the ball, we have been camped in their half for long periods," he said of the performance.
"The first goal is clearly offside and the second goal is either an outstanding shot or a fluke, I think it's a fluke.
"So we are disappointed with the result and the manner of the goals we conceded.
"But I thought we deserved something out of the game. We are very disappointed, but I am not going to keep saying we nearly should be getting results, enough is enough.
"It's down to the quality of players to stick together and keep producing chances and keep trying to convert them.
"If you've seen us over the three games people can't fault the style of play, once we get a goal up or a refereeing decision goes our way we will see a different team.
"If you look back over the three games, the key moments are going against us and the tide will turn for us eventually."
The win was Dickov's first league victory in charge of Doncaster and his opinion of the game could not have been any more different.
The Scot, who was appointed to the role in the summer, believed his side were worthy winners and was delighted to get the win tally ticking over.
"For the majority of the game we were excellent," he said.
"It's fantastic to get the three points and win at home. Defensively we were so solid and astute with how we dealt with Blackburn because they are a good team with good players.
"It's important to get the first win because the longer you go without winning, the more people start to panic.
"For our fans to see a performance like that it will give them belief that we are a good team.
"I don't want to put a downer on it but I believe we are better than what we showed tonight.
"We want to set good standards. We can improve all over, I can't believe that we have won 2-0 and I am talking about how we can improve."