The Windows system-maker had alleged its rival had infringed a way to let applications talk to a handset's radio communications hardware.
The German court's ruling ends a run of three previous patent victories scored by Microsoft over Google this year.
However, it has little practical effect since Microsoft has already secured bans against several Motorola products.
These include sales restrictions preventing stores offering about a dozen devices including the Droid Razr and Razr Maxx handsets.
The latest case involved software application programming interfaces (APIs) used to allow software developers to write a set of code guaranteed to work with different mobile devices' radio antennas.
Potential uses include letting a mobile phone select a network operator; transfer a call; send and receive a text message; and access individual files stored on the Sim card.
Microsoft laid claim to the methodology in a filing submitted in 2002.
The judge did not explain his reason for rejecting the claim.
Microsoft had previously won German cases based on separate patents related to SMS messages, a way to handle user-input and use of the file allocation table (Fat) file system architecture.
"This decision does not impact multiple injunctions Microsoft has already been awarded and has enforced against Motorola products in Germany," said David Howard, associate general counsel at Microsoft.
"It remains that Motorola is broadly infringing Microsoft's intellectual property, and we hope it will join the vast majority of Android device makers by licensing Microsoft's patents."
A spokeswoman for Google said: "We are pleased with today's favourable outcome for Motorola Mobility, but won't be able to provide more specific information on this matter."
While Microsoft dominates the PC operating system market, it is a relatively small player in the fast-growing smart device sector.
Thanks to the success of its Android software, Google's system powered 68.1% of global smartphone handsets in the April-to-June quarter, according to a study by Canals.
By contrast Microsoft's Windows Phone system had a 3.2% share.
But Microsoft makes money from most Android device sales as it has struck patent licensing deals with other handset makers, including Samsung and HTC, for the use of its technologies in the system.
When Google decided to buy Motorola it said that the action was chiefly driven by a desire to own its 17,000 patents.
The move has allowed it to directly challenge Microsoft and others' claims to set a precedent for other firms using its software, albeit with mixed success.
Motorola has scored its own victories. Earlier this year the division won the right to prevent Germany's stores from selling Microsoft's Xbox 360 games consoles, the Windows 7 operating system, the Internet Explorer browser and Windows Media Player.
However, it has not been able to enforce the ban and faces a related hearing next month.
Meanwhile the two firms are involved in a series of other intellectual property fights in the US. These have already led to an import ban being placed on some Motorola devices.
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