Probably late: US Courts don't over-ride German courts, but for multi-national organizations like Microsoft and Motorola, they can't act with legal independence in specific countries that have differently defined laws without also having those issues come to a head in other countries. A US Court is saying, "hold on Motorola," and Motorola -- as a multi-national organization -- is following their best interest by "holding on." Not only that, but Microsoft can appeal, and this would probably take effect like 5+ years after the ruling, even if the appeal was upheld. With major companies and major products, these always end in settlements or international agreements (ie, Microsoft can license the Motorola product in their next console for $X agreement).
This isn't US superceding German courts, it's international business, and both companies have international interests.
*edit*
For the cynics: The same idea protects, say, European stakeholders who hold stock in primarily American companies that merge... This is why the EU can reject a major acquisitions and prevent the merger in the United States, despite both companies being primarily American companies. It's not that European courts would be over-ruling American law or American courts, but rather, that both companies have European interests, and have to consider them for their best interest as multi-national organizations..
And, again, this wouldn't be a ban in Germany. Even if the ruling were upheld, which it probably wouldn't be, it would result in a nominal settlement.