Rovers were awarded a controversial late penalty after Grant Hanley was fouled in the area by Danny Shittu and Jordan Rhodes made no mistake from 12 yards, earning his side all three points in their fight against relegation.
Bowyer told reporters: "I don't think we should be talking about that. We should be talking about our second-half performance and how brave my players were. Some you get, some you don't.
"Are we safe? No. It's crazy with 56 points but no, we aren't."
Blackburn are 15th in the Championship, five points clear of the relegation zone with two games to play.