The Scotland international was adjudged to have been tripped by Danny Shittu in the area and Jordan Rhodes stepped up to move Rovers five points clear of the drop with two games to play.
Millwall boss Kenny Jackett accused Hanley of diving, but Bowyer preferred to focus his attention elsewhere after his side's first away win in the league since December.
"I don't think we should be talking about that," he said when asked about the incident. "We should be talking about our second-half performance and how brave my players were. Some you get, some you don't.
"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."
Despite his side's third win in four games, Bowyer did not believe they had escaped the drop just yet.
"Are we safe? No," he added. "It's crazy with 56 points but, no, we aren't."
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