The latest ruling by Boston district court judge Mark Wolf comes a week before Microsoft faces the EU's second highest court to appeal against a 2004 ruling that it had abused its dominant market position.
'Ignoring the rules'
"Enforcing Microsoft's ... subpoena to Novell would circumvent and undermine the law of the European Community concerning how a litigant may obtain third-party documents," judge Wolf said in his 12-page decision.
Last month, the software giant asked US federal courts to force four of its rivals to hand over documents relating to the European case.
However, its attempts to subpoena sensitive information from Oracle and Sun Microsystems were quashed by a Californian judge last month.
A New York judge is currently considering a request against IBM.
Brussels has ordered Microsoft to open up its software code to rivals, threatening it with daily fines if it was found to be dragging its heels over the issue.