The flaw, spotted by Luxembourg-based security expert Eric Romang, makes machines vulnerable to the Poison Ivy trojan, used by cybercriminals to steal data or assume remote control of a PC.
Microsoft's Fix It tool is intended to be a temporary solution while a fully-fledged security update is developed.
"This is an easy, one-click solution that will help protect your computer right away. It will not affect your ability to browse the web, and it does not require a reboot of your computer," said Microsoft in a blog post.
The computing giant claims that an "extremely limited number" of users were subjected to Poison Ivy trojan attacks, and noted that Internet Explorer 10 users have not been affected at all.
Liam O Murchu, research manager with security company Symantec, points out that so-called zero-day or security failings are concerning because of their novelty value to cybercriminals.
"Any time you see a zero-day like this, it is concerning," BBC News quotes him as saying. "There are no patches available. It is very difficult for people to protect themselves."
The Fix It tool is available to download now through Windows Update and other standard distribution channels.