Bowyer felt Rovers could have been awarded a penalty when Josh Morris appeared to be fouled by Kagisho Dikgacoi early in the second half.
But he also admitted Palace had a strong penalty claim waved away as well, in what was an exciting match at Ewood Park.
"It's a good point against very good side," Bowyer said.
"They're an attacking team and play a passing game but I thought we matched it at times and played some good stuff ourselves. With a little bit more care in the attacking third, we might just have won it.
"We had a great shout for a penalty when Morris got brought down. It was a stonewaller for me, though Palace had a good shout for a penalty too.
"But we've shown against a good team how close this championship is. We're delighted with a point but maybe we could have got three."