However Ruben, fourth in race one, held firm and collected his first ever 1098 win, and first WSBK victory since Valencia 2007, by one second from the former MotoGP star.
Bayliss settled for his second third place of the day ahead of R1 team-mates Haga and Corser, with Lorenzo Lanzi sixth for the RG Team.
Neukirchner was unable to reproduce his race one form, but was still the top GSX-R1000 rider in seventh, with Hannspree Ten Kate Honda's Carlos Checa the leading Fireblade in eighth.
Bayliss' team-mate Michel Fabrizio, who collided with Biaggi in race one, had suffered an engine failure on lap one of race two - but was given a second chance by the restart. The Italian had been fighting in the lead group until his race one accident, but managed just eleventh on his spare machine.
In the world championship standings, Bayliss is now 49 points in front of Neukirchner, with Checa three points further back and Haga 68 from the top.
Misano race two: