Both were sent tumbling into the gravel, Checa remounting to finish fifth, but a devastated Neukirchner was trapped momentarily under his bike and never reached the flag.
Out of sight, Lanzi had skillfully overtaken Bayliss for what looked like being the final podium position - which then began first place following the drama ahead.
Lanzi's victory was his third in WSBK, but first since 2005 - the Italian having endured two nightmare seasons with the factory squad prior to joining the satellite RG outfit for 2008.
Troy Corser completed the podium, while the third Alstare Suzuki of
Fonsi Nieto - currently second to Bayliss in the world championship standings - survived the chaos ahead to climb from 13th on the grid to fourth position at flag, but he's now slipped to 34 points behind Bayliss in the title fight.
The injured Max Biaggi, who began the race in ninth position, lost out on the chance to capitalise on the incidents ahead after running down an escape road, while holding tenth place, on lap seven - dropping him to the back of the field. The Roman went on to finish out of the points in 16th.
Valencia race one
1. Lanzi
2. Bayliss
3. Corser
4. Nieto
5. Checa
6. Muggeridge
7. Lavilla
8. Laconi
9. Tamada
10. Rolfo
11. Nakano
12. Sofuoglu
13. Holland
14. Smrz
15. Checa
16. Biaggi
17. Badovini
18. Morelli
19. Lozano Ortiz
20. Napoleone