Bayliss, who currently holds a commanding 70 point lead and will retire from WSBK at the end of this season, surged forward from just eighth position at the end of second qualifying with a blistering Superpole effort, during which his 1098 F08 - appropriately sporting the #21 - effectively matched the top speed of its four-cylinders rivals.
The Australian will be joined on the front row by Suzuki's man-of-the-moment Max Neukirchner, Yamaha's 2007 double Monza winner Noriyuki Haga and Honda's star rookie Carlos Checa.
"It's been a bit of a mixed weekend, we've been struggling a bit with the race tyre but we've worked hard, trying different things and finally it's come quite good," said Bayliss. "We were down a little way this morning but made a few changes and now we are much more consistent on the race tyre.
"I was very happy with the lap I did in Superpole. I thought it was possible Nori or Max could do a little faster, but they made tiny mistakes and that was enough to keep that lap. I also made a little mistake in the first chicane when I ran wide but it came together good.
"Tomorrow will see some tough racing, Max is consistent on the tyre and proving to be a real contender. It's very difficult to get away at Monza, I have a feeling it's going to be between Max, Nori and myself but I'm sure it's going to be more than that for the first eight laps," he predicted.
Saturday was a more problematic day for team-mate Michel Fabrizio, who had difficulty finding the right set-up for his home event. Losing valuable tenths at certain points of the track, such as the final Parabolica curve, continued to be an issue and the team will make further modifications to the Italian's machine.
"It's been really quite difficult this weekend and I am disappointed with the Superpole results of this afternoon," admitted Michel, who will start from 13th. "I hoped to go faster, at least going under 1min 46 but it didn't happen. Just like yesterday I continued to lose time in today's sessions through the Parabolica curve and then made a couple of other little mistakes which meant I was unable to secure the starting position for the races that I hoped for. We'll make a few more changes tomorrow morning because I just didn't feel quite right today with the bike. On a positive note, my arm is not giving me any trouble so that is good news."