Rovers hugely eased their relegation worries with a 2-1 victory at the Den, fighting back having been a goal behind at half-time, and bagging the three points when Jordan Rhodes scored from the spot with 12 minutes left.
Referee Gavin Ward gave the spot-kick after deciding Danny Shittu had tripped Grant Hanley in the area but Millwall were adamant that the Blackburn man had dived.
However, Bowyer said: "I thought it was a great run from Hanley, he deserves credit for that and, from where I stood, I jumped up because I thought it was a penalty.
"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."
Blackburn are now five points clear of the drop zone with only two games left but Bowyer is in no mood to relax.
"Are we safe?" he said. "No. It's crazy with 56 points but no, we aren't."