The Italian leapt to the top of the time sheets on his final lap as the leaderboard continuously changed during the dying minutes.
In a good session for Italian bikes, Aprilias and Ducatis made up the top five with Biaggi edging out Michel Fabrizio by a tenth of a second, followed closely by Carlos Checa, Noriyuki Haga and Shane Byrne.
Byrne had been the pace setter through much of the session as he became the first rider to dip into the one minute 56 seconds bracket, though he failed to improve as the track rubbered in later on.
Last year’s Nurburgring race winner Jonathan Rea was sixth fastest on the Ten Kate Honda, ahead of fellow Britons Cal Crutchlow and Leon Haslam, both of whom moved up the order late on having sat outside the top 10 for much of the hour.
Troy Corser and Lorenzo Lanzi completed the top 10 positions.
Further back, James Toseland was 14th on the second Yamaha, ahead of Nurburgring rookie Leon Camier in 16th, while Tom Sykes was 17th having been unable to improve on an earlier lap time that had placed him comfortably inside the top 10.
Ian Lowry was a solid 19th on his WSBK debut, the Ulsterman less than seven tenths adrift of his more experienced Kawasaki team-mate. He also fared better than fellow WSBK newcomer Fabrizio Lai, who was 21st on the Echo CRS Honda.