The one-hour session was marked by a qualifying duel between Bayliss and Neukirchner's team-mate
Yukio Kagayama, but three minutes from the end the 25-year-old clinched provisional pole after a tow from Kagayama.
Makoto Tamada, making his debut at the Autodromo Nazionale, also looked impressive on the PSG-1 Corse Kawasaki machine on the long Monza straights, the Japanese rider clocking the fourth quickest time.
Friday's second row also produced a few surprises, with morning pace setter Jakub Smrz (Guandalini Racing Ducati),
Karl Muggeridge (DF Racing Honda) and
Kenan Sofuoglu (Hannspree Ten Kate Honda) finishing ahead of
Michel Fabrizio (Ducati Xerox)), who is recovering well from his recent operation to reduce arm-pump.
but the day was a disappointing one for last year's double winner
Noriyuki Haga, who could go no better than 12th quickest for Yamaha Motor Italia, while Hannspree Ten Kate Honda's
Carlos Checa - currently second to Bayliss in the world championship standings - was a further two places behind in 14th.
Sterilgarda Go Eleven Ducati rider Max Biaggi's recent difficulties continued on Friday, with the Italian star only 17th fastest.
Friday qualifying- top 15:
1. Neukirchner
2. Bayliss
3. Kagayama
4. Tamada
5. Smrz
6. Muggeridge
7. Fabrizio
8. Sofuoglu
9. Xaus
10. Lavilla
11. Nieto
12. Haga
13. Laconi
14. Checa
15. Corser
