Pastor Maldonado put in the perfect lap at the perfect time on an almost-dry Hockenheim circuit to take the P1 slot ahead of Nico Rosberg.
Friday's second practice saw the timesheets largely decided by who was out on track in what conditions, the Williams driver clocked a 1:27.476 moments before the rain came down washing out was left of the session.
Rosberg finished second, 0.088s down while Sebastian Vettel, who was yet to win a German Grand Prix, was third, 0.426s off the pace.
With the rain coming down at the start, Practice Two didn't even get off to a slow, it got off to no start as the drivers opted to wait out the weather in their respective garages.
After 20 minutes the first time was finally set by Jean-Eric Vergne, one of only four drivers who had even braved the conditions. He clocked a 1:43.330.
Nico Rosberg was the next to lead the way, warned about "rivers" by his Mercedes pit wall, before losing out to Vergne. That started a brief tussle between the two for the P1 slot as the drivers aquaplaned and the lap times came down.
Their battle ended when Sebastian Vettel went quickest followed by Michael Schumacher, who brought the benchmark time down to a 1:38.194.
The two Germans lost out to Vergne before another German, Rosberg, hit the front only to be beaten moments later by Fernando Alonso. Rosberg responded by setting another fastest lap time only for Alonso to again better it, this time by a massive 1.2s. The Ferrari driver was leading at the halfway point with a 1:34.593.
Felipe Massa was the next to lead the way before Sergio Perez, then Daniel Ricciardo, then Romain Grosjean, then Michael Schumacher, again Grosjean and then Alonso overhauled him. The benchmark was down to a 1:31.207.
Despite a few slips and slides the drivers continued lowering the benchmark as the track dried down. Massa had a turn at the front as did Perez, Raikkonen, Vettel and then Button, who had been quickest on a dry track earlier in the day.
However, when the rain came down with 27 minutes on the clock it was Maldonado who was in the P1 slot with a 1:27.476. Rosberg was second ahead of Vettel, Perez, Grosjean and Hulkenberg.
Some drivers ventured out in the final 20 minutes as the rain let up to get a feel for the wet running as there is a possibility of rain on Saturday. However, none were able to improve on their lap times while Ricciardo's off into the gravel - which left him beached - highlighted the tricky conditions.
The session was stopped with four minutes on the clock when Schumacher suffered a heavy crash. Schumacher touched the outside line, lost control of his car, crashed nose first and was spun until the rear also hit the barrier.
01 Pastor Maldonado Williams 1:27.476 14 laps
02 Nico Rosberg Mercedes 1:27.564 0.088 24 laps
03 Sebastian Vettel Red Bull 1:27.902 0.426 24 laps
04 Sergio Perez Sauber 1:28.402 0.926 26 laps
05 Romain Grosjean Lotus 1:28.420 0.944 20 laps
06 Nico Hulkenberg Force India 1:28.495 1.019 22 laps
07 Daniel Ricciardo Toro Rosso 1:28.513 1.037 23 laps
08 Jenson Button McLaren 1:28.516 1.040 16 laps
09 Mark Webber Red Bull 1:28.877 1.401 21 laps
10 Kimi Raikkonen Lotus 1:29.327 1.851 22 laps
11 Jean-Eric Vergne Toro Rosso 1:29.364 1.888 26 laps
12 Felipe Massa Ferrari 1:29.719 2.243 15 laps
13 Kamui Kobayashi Sauber 1:29.785 2.309 24 laps
14 Charles Pic Marussia 1:30.090 2.614 19 laps
15 Timo Glock Marussia 1:30.220 2.744 16 laps
16 Bruno Senna Williams 1:30.291 2.815 22 laps
17 Heikki Kovalainen Caterham 1:30.331 2.855 26 laps
18 Paul di Resta Force India 1:30.437 2.961 14 laps
19 Lewis Hamilton McLaren 1:30.617 3.141 16 laps
20 Fernando Alonso Ferrari 1:31.207 3.731 20 laps
21 Vitaly Petrov Caterham 1:32.241 4.765 22 laps
22 Narain Karthikeyan HRT 1:32.349 4.873 17 laps
23 Michael Schumacher Mercedes 1:32.777 5.301 18 laps
24 Pedro de la Rosa HRT 1:42.566 15.090 8 laps