The 25-member bloc stressed that the suspension was an "interim measure" until a court had ruled on Microsoft's request.
The company has also asked for a long-term suspension of EU-imposed changes to the way the firm operates.
These changes include selling a version of Windows without its media player software and a requirement to unbundle the software within 90 days. The deadline runs out on Monday.
In its March ruling, the EU also handed Microsoft a record fine of €497m and gave it 120 days to reveal details of its Windows software codes, so rivals could design compatible products more easily.
But on Friday, the company appealed to the Court of the First Instance in Luxembourg, asking it to suspend the orders for as long as its case remains before the European Courts.
That could see the penalties suspended for as long as three years.
But the European Commission added that the decision to put the punishment on hold was "without prejudice to Microsoft's obligation to implement the remedies" if the court decides to reject the company's request.
Rivals, including Real Networks, have complained that Microsoft was unnecessarily bundling in software with its operating system, and as a result gaining an unfair advantage.
One of the main bones of contention was Microsoft's media player - software used to play audio and video, as well as to burn CDs.
However, Microsoft has vowed to fight the Commission's finding that it had broken competition laws, arguing that the EU sanctions will stunt competition and innovation and limit consumer choice.
Microsoft's Windows software runs on about 90% of the world's PCs.