The company said it filed the re-hearing request with an appeals court because it believes the ruling was based on "clearly erroneous" findings of a lower court judge.
At the time the lower court had condemned the bundling of Microsoft's Internet Explorer with Windows as a move to head off competition from rival browsers.
Three weeks ago, the US Court of Appeals ruled that Microsoft had operated as an illegal monopoly, but it reversed an earlier order by the same lower court to break up the company.
The Court of Appeals also sent the case back to a different lower court judge to decide a new penalty.
Legal options
After the ruling, either side was given the option of asking the appeals court to reconsider parts of the decision, appeal against the entire ruling to the Supreme Court, settle, or go back to a lower court.
The company said the new petition was "a good-faith attempt to seek clarification," and should not be read as an unwillingness to settle the landmark antitrust case out of court.
Microsoft feels that the Justice Department, the US' main anti-trust body, has not justified its claim that bundling browser code into the Windows system violated competition rules.
For the software giant, the issue affects its whole product strategy and the freedom to add new features to the Windows operating system.
Speed
Last week, the Justice Department moved to speed up the antitrust case, asking the appeals court to immediately send it back to a lower court for reconsideration.
The department said it does not intend to appeal to the Supreme Court at this time.
The lower court to which the case has now been referred is expected to be more sympathetic to Microsoft, as it had previously ruled in Microsoft's favour in a different but similar case.