Rovers have not won a match since the middle of February, with Jermaine Johnson netting Wednesday's winner 12 minutes from time.
Jordan Rhodes had fired Blackburn ahead from the spot before Johnson levelled matters midway through the first half.
Leroy Lita's penalty sent the Owls in at half-time with a 2-1 advantage while Scott Dann drew Blackburn level.
Bowyer said: "One or two of the decisions haven't gone our way. Ours was a definite penalty but for their penalty their lad goes down like he has been hit by a truck.
"The linesman possibly crumbled under the pressure a bit. These are the things that change games.
"We aren't going to feel sorry for ourselves as it's in our hands still - we have a game in hand.
"Of course it's difficult, it's a difficult situation, but I'm not going to shirk. I'm going to give it my best shot and the players care, they really care.
"Our games are winnable games. We can get 18 more points but our luck has to change."