The Australian arrived at Assen a little worse for wear after a pushbike accident while training back home in Monte Carlo.
But the double champion brushed this all aside in typical style to be quickest in first qualifying aboard the Xerox Ducati.
Bayliss only led the session in the latter stages though as Jakub Smrz was heading the timesheets for most of the session before Bayliss managed to put together a very good lap right at the end to dip into the 1m39s bracket and claim the top spot.
The 1999 British Superbike champion is well aware however that the field is very tight behind him and further work is necessary to keep the pack at bay.
"It's the first time I have ridden the 1098R here," Bayliss said. "We made good progress today and have moved progressively in the right direction.
"There are a few things I would like to try tomorrow, but like everyone else that depends as usual, on the weather here in Holland.
"This track always makes for close racing so if we can make some more improvemnts to smooth out my riding then I'll be right there."
Second rider in the team,
Michel Fabrizio had a difficult day, interrupted by a small spill in the first practice period which meant he could only use one bike. The Italian was unhurt.
"I had a crash this morning," revealed the Italian. "I was exiting a bend and didn't see a wet patch in time and dropped the bike. This compromised me as I had to use the second bike which we had not worked on too much before then.
"This afternoon was better, back on the first bike again. My time would have been better but for the red flags later on too. But, we have things to try tomorrow to go quicker."
