Both sides had chances to snatch the three points, though a draw was a fair reflection of the game.
Jordan Rhodes forced a smart save from Chris Kirkland in the first half and Rudy Gestede sprinted clear early in the second half before being thwarted by Kirkland.
Despite the stalemate, Rovers are well in the hunt for a place in the top six and are now unbeaten in four - something Bowyer believes should not be forgotten.
He said: "I think that's six out of the last nine games we've kept a clean sheet, three in the last four games. We're unbeaten in four games. There's a chorus of boos around the ground which I don't quite understand because we have to remember where we've come from and where we are now and how much further we can go.
"Their goalkeeper has worked very hard to keep Jordan out a couple of times. Josh King shot straight at him, Rudy should do a little bit better when clean through but I'd be more concerned if we weren't creating these chances.
"Over the course of this season it could be a big point."
The stalemate ended Blackburn's run of two straight wins and Bowyer felt his side were not ruthless enough in front of goal.
"I think points are very difficult to come by in the Championship and we have to respect the point today," Bowyer said. "We created some good chances, not enough chances but we just weren't ruthless enough in front of goal.
"I think you always try to win the game but if you can't get the three points, make sure you get the one. There have been several times this season when people have said to me 'last season we wouldn't have got the draw', so the progress we're making is decent."
Sheffield Wednesday caretaker manager Stuart Gray paid tribute to his side after securing a second consecutive away clean sheet.
Having failed to win any of their first nine games on their travels, the Owls have now picked up four points from their last two away trips and could have taken all three points at Ewood, but Simon Eastwood made two terrific saves in the first half to deny Atdhe Nuhiu.
And though Gray was slightly frustrated his side could not quite find a winner, he feels the signs are more than positive.
He said: "I thought we had the better of the first half, had the better chances. Atdhe is unlucky not to score - a couple of good saves by their goalkeeper. And the only time they got in it was self-inflicted.
"In the second half I felt it was two teams who cancelled each other out.
"It's nice to get a clean sheet. We've had back-to-back clean sheets away and you can't undervalue the point.
"Disappointing that we didn't get our noses in front at half-time. But like I said to the players, individually they've put performances in and collectively defended as a team. The most important thing is that we got the point.
"In the second half we probably lacked a little bit more guile in front of goal, snatching at things instead of just picking out the better pass.
"I thought the two centre halves kept Jordan Rhodes very quiet. When you come to Blackburn, 95% of their goals probably come through Jordan, so credit to the defenders."