The patch can be downloaded from Apple's website or through its Software Update feature in the operating system.
The problem was discovered by software developer Wolfram Research. It alerted its customers when it found that the patch caused its Mathematica 5.2 application to stop working.
"Due to an error on the part of Apple, this update prevents any 64-bit-native application from running. In particular, this means that Mathematica 5.2 will not run on any G5 system if it has installed this Security Update," the company told customers.
"This problem was discovered by our testing procedures a few hours ago, and Apple has now assured us that they have stopped automatic distribution of Security Update 2005-007 at this time."
The problem, fixed with the new release, was caused by the omission of a 64-bit version of the LibSystem component, which forms an important part of the OS's BSD layer.
The security update earlier this week was one of the biggest ever released by Apple, with patches for more than 40 flaws.
Earlier this month, Microsoft released six security patches for Windows in its regular monthly security update.