Shaun Williams put the hosts ahead from the spot, following a foul that earned Grant Hanley his marching orders, but Rovers' on-loan defender Michael Keane soon headed his side level.
Simeon Jackson thought he had won it for the hosts, netting Millwall's second penalty after being brought down by Keane, but substitute Josh King struck in stoppage-time to deny them a second win in 13 games.
However, Bowyer found it tough to accept referee Nigel Miller's judgement on either penalty and felt Rovers deserved the win.
"We've conceded 10 penalties away from home this season," Bowyer said.
"Our lad says he got a touch on the ball first and then takes him down for the second penalty, but hey if he gives the first he's going to give the second isn't he? If that's a penalty you're going to have 10-15 penalties a game.
"It was outstanding character and belief (to equalise). Their desire, belief and mentality was outstanding but unfortunately it wasn't enough because of the referee's decision.
"The quality of our football and goals is there for all to see but it's very difficult to talk about the positives all the time.
"I sincerely hope that the point that Millwall got keeps them up because I love coming here. It's a brilliant football club, they have a great manager and it's a fantastic environment for football.
"The passion and desire for their football club is just outstanding so I really hope they stay up."
Millwall manager Ian Holloway felt as though his side had lost the match, though he was not quick to disagree with his opposite number on the game's key decisions.
"We feel like we've lost in there but we've only dropped two points," he said.
"We've got to win five out of seven now but we should have won this one. I'm fuming because we've dropped two points but we did get one.
"We live to fight another day. How am I going to feel when I drive home tonight? I'll be devastated when I see that on television but when I say devastated, it's because it's easily solvable.
"We are where we are for these reasons and we need people now to step up to the plate.
"Truthfully, I thought the first one and the sending off was nowhere near as bad as some of the things I've seen recently.
"If it was a penalty then it's only a yellow card. I don't understand but we've scored them both which is nice - makes a change."