A judge ordered a block on the Joint Enterprise Defense Infrastructure (JEDI) initiative, a huge effort to modernise the USA military's computer systems, which the Department of Defense had awarded to Microsoft in October.
The government can't proceed with implementing the contract "until further order of the court", according to the decision by U.S Court of Federal Claims Judge Patricia Campbell-Smith.
Details of the ruling were sealed for unspecified reasons.More news: The scope of Christina Koch’s work after nearly a year in space
The JEDI contract has been hotly contested not only because it is worth an estimated $10bn, but also because the green light from the U.S. military would be a significant vote of confidence that any victor could use to win further deals.
Bezos also owns the Washington Post, whose coverage has been critical of Trump and which has frequently been a target of barbs by Trump about the news media.
Microsoft told The Register it remains confident the JEDI - aka the Joint Enterprise Defense Infrastructure - cloud contract will go forward with Redmond at the helm.More news: Kobe Bryant honored at 2020 Oscars
Microsoft said it hoped to prevail after the merits of the case are heard in court. Among the leaders Amazon seeks to depose are Trump, former Defense Secretary James Mattis, Defense Secretary Mark Esper and Dana Deasy, the Pentagon's chief information officer.
Amazon argued in court documents that the Pentagon's choice of Microsoft was mystifying if not for Trump's repeated "expressed determination to, in the words of the president himself, 'screw Amazon'".
The contract in question, for cloud computing services for the military, is among the Defense Department's biggest and it drew legal challenges over the procurement terms even before it was awarded.
"We have confidence in the Department of Defense, and we believe the facts will show they ran a detailed, thorough and fair process in determining the needs of the warfighter were best met by Microsoft", said Frank Shaw, the company's vice president of communications.More news: Damian Lillard to miss All-Star weekend, hopes Devin Booker gets his spot
She also ordered Amazon to set aside $42m for costs if future proceedings found she was wrong to have issued the injunction.