Championship leader Rosberg, whose advantage over Hamilton was cut to four points after he failed to finish at Silverstone in a race won by the Briton, bounced back well by setting a time of one minute and 16.540secs to head the grid.
And Hamilton's misfortune made it a doubly successful afternoon for Rosberg at Hockenheim.
The 2008 world champion was sent spinning into the barriers in the first session due to a brake disc failure in what could prove to be a turning point in a fascinating two-horse race for the title.
Hamilton had already set a time good enough to qualify for the second stint, but the crash meant he was unable to compete in the rest of qualifying, leaving him to settle for a disappointing 15th on the grid, taking a grid penalty for Sauber's Esteban Gutierrez into account.
Mercedes' dominance so far this season was not reflected in the first qualifying run since front-and-rear interconnected (FRIC) suspension systems were outlawed, with Williams looking potential challengers to Rosberg.
Valteri Bottas was second, just two tenths of a second behind Rosberg, while team-mate Felipe Massa (1:17.078) rounded off the top three.
Rookie Kevin Magnussen (1:17.214) was another impressive performer as he took fourth, reversing a recent trend of being often out-qualified by McLaren team-mate Jenson Button, who could only go 11th-fastest.
Daniel Ricciardo (1:17.273) was fifth and defending champion Sebastian Vettel (1:17.577) was sixth as Red Bull locked out the third row of the grid.
Fernando Alonso (1:17.649) claimed seventh, enjoying a better outing than fellow Ferrari driver Kimi Raikkonen.
Raikkonen, whose car was hit by fuel-pump problems in practice, failed to make the top-10 shoot-out, qualifying 12th to offer little hope of the Finn adding to his meagre total of 19 points.