The German edged out Alstare team-mate Yukio Kagayama by 0.126secs to take provisional pole, the Japanese making an impressive return to action after missing the previous Phillip Island round due to injury.
Having made a spectacular entry to his first home event as a WSBK rider, when he parachuted into the Valencia circuit on Thursday, Carlos Checa continued his 'flying' form with the third fastest time on his Hannspree Ten Kate Honda - just 0.236secs from the top.
Double World Superbike champion and 2008 title leader Troy Bayliss may have missed the recent Valencia test to recover from his injuries, but the Australian proved he'll be at little disadvantage as he set the fourth fastest lap time, just 0.018secs behind Checa and 0.020secs in front of Ducati Xerox team-mate Michel Fabrizio.
Fabrizio, another test absentee due to injury, enjoyed a strong second session after being just 24th fastest during morning free practice.
Fellow Italian Max Biaggi, who broke his wrist at Phillip Island, was twelfth fastest this morning, but slipped to 24th during the afternoon as his injury began to bite. Having been eighth in FP1, Sterilgarda Go Eleven team-mate Ruben Xaus also faded during the afternoon, the 2007 Valencia winner being ranked just 17th on the overnight grid for his home race.
Fellow satellite 1098 rider Lorenzo Lanzi - who, like Xaus, had attended the recent Valencia test - had a far more promising day, claiming fifth in the morning and then sixth in the afternoon on his RG Racing machine. Czech Jakub Smrz was seventh quickest, making it four 1098s in a succession on the provisional grid.
Kawasaki PSG-1 riders Regis Laconi and Makoto Tamada bounced back from a difficult morning session to claim eighth and twelfth in first qualifying - with Yamaha Italia team-mates Troy Corser and Noriyuki Haga, plus Checa's team-mate Ryuichi Kiyonari sandwiched between the ZX-10Rs.
While team-mate Neukirchner and Kagayama were setting the pace, team-mate Fonsi Nieto - currently second to Bayliss in the world championship standings and the only other WSBK race winner so far this year - was just 16th fastest after struggling with rear tyre grip.
