The Briton's 1m16.595s lap was 0.498s faster than his team-mate Lewis Hamilton, with championship leader Fernando Alonso third on the timesheets for Ferrari.
Intermittent rain showers rendered times fairly irrelevant in terms of determining form, with teams frequently having to cut short evaluation runs for the updates they have brought to Germany. Button's time was set when the track was completely dry in the first 20 minutes of the 90.
Of the established runners, only he and Lotus driver Romain Grosjean got their programmes running before precipitation played its part.
When Sergio Perez, Mark Webber and Heikki Kovalainen all then ran wide, however, it was a clear signal that the asphalt was no longer dry and this set a pattern for the rest of the session.
With short, sharp showers dampening the track and then warm ambient temperatures quickly drying it again, the surface became dry enough for teams to continue, if somewhat stutteringly, with their programmes on the medium and soft compounds. During this point, Nico Hulkenberg and Alonso improved to go second and third behind Button.
Unsurprisingly, almost every driver had a moment at some point as the grips levels changed constantly.
The heaviest of these showers came 20 minutes before the end, prompting Sauber's Perez and Kamui Kobayashi - who had a significant moment running across the gravel early on - to try intermediates. That plan was swiftly scuppered though after an exploratory lap each.
The last 10 minutes provided some of the driest running and also a flurry of activity on the timing board as Hamilton went second quickest to make it a McLaren one-two. Alonso improved again to go third with Michael Schumacher's Mercedes fourth.
Perez also squeezed ahead of Hulkenberg before Valtteri Bottas crashed Bruno Senna's Williams at the Sachs Kurve with three minutes to go. That scuppered any hope of anyone going quicker through the final sector - including Hamilton, who was fastest of all through S2 on his final lap.
Nico Rosberg was seventh ahead of Felipe Massa, Pastor Maldonado and Grosjean.
The Red Bulls had a low-key session, with world champion Sebastian Vettel 12th and Webber 20th. Kimi Raikkonen was 15th in the Lotus, running with the new double DRS system, having only completed 14 laps in total.