Rovers couldn't find a way through a well-drilled, defensively-minded Wednesday side, as they frustrated the Lancastrians, but the point made it four unbeaten for Bowyer's boys and a third clean sheet in four.
Speaking to Radio Rovers after the game, Bowyer said that the Owls payed his side a massive compliment by coming to Ewood and playing in such a manner, indicative of how far his young side have come.
"The lads are disappointed and frustrated but over the Christmas period you shouldn't disrespect any point that you pick up," said the Rovers boss.
"I think you have to take the game on a whole, Sheffield Wednesday came with a game plan, they put five across midfield and they haven't been doing that recently.
"They've beaten Leicester City and Watford in the last month so it was never going to be an easy game and we knew that, but it is frustrating that we couldn't convert one of the chances that we had.
"They paid us a massive compliment with that, and I was a little bit disappointed towards the end of the game where there were boos going round the ground, but the fans have to realise that it is for us to break them down, but teams are now coming here with a lot of respect and a game plan to stop us playing.
"I think if you look at where we have come from, to have that in the short space of time is massive progress for us as a football club.
"It is a touch disappointing to hear boos but we'll dust ourselves down and go again, we've an important game against Birmingham and we need the supporters behind us.
"You might see how valuable this point could be come the end of the season."
Rovers are back in action this Sunday when Birmingham City are the visitors to Ewood Park.
Tickets are currently on open sale with prices from £19 for Adults, £12 Seniors and £7 Juniors. Book online today at www.onerovers.co.uk
and collect your tickets from the Blackburn End collection point at the end of the game.