The move highlights the growing rivalry between the two Silicon Valley giants as they encroach on each other's territory in the mobile phone market, while raising questions about Apple's authoritarian app approval process.
Apple declined to comment on the matter, but a Google spokesman said its Google Voice app was outright rejected from the App Store.
Google Voice allows users to send free SMS text messages and offers very cheap long distance calling, while allowing customers to merge all of their mobile phone and landline numbers under a single Google Voice number. The service also translates users' voicemail into a readable text message.
Google Voice uses a regular mobile network connection, then routes the call to the internet destination -- different than Skype, which simply requires a WiFi connection.
The app is available for Google's Android-based mobile phones and Research In Motion's (RIM) BlackBerry.
Google Voice has been met with genuine enthusiasm in the tech industry. Bloggers yesterday were surprised that the app had been rejected, many speculating that US mobile network AT&T was behind the deed.
Jason O'Grady, a blogger from ZDNet, wrote: "It's pretty obvious that AT&T is behind the Google Voice ban on the iPhone because the app is a potential game-changer and AT&T is scared silly of it.
"It allows people to call you on your [Google Voice] number (regardless of which carrier you are using), send free SMS messages and get cheap long-distance too -- all big time threats to AT&T's iPhone cash cow."
Despite the theory, the app's rejection shows the increasingly un-neighbourly relationship between the two companies.
Just last week, Apple rejected another of Google's apps -- its location-based software Google Latitude.
This month, Google revealed it is developing a computer operating system to compete with Apple's own OS.
Apple's approval process for its App Store has long been criticised for its fair-weather policies and heavy-handed rejections.
Despite this, more than 50,000 iPhone apps have been created, resulting in over a billion downloads -- providing a cash boon for both Apple and software developers.
Google said it would continue to work to bring Google Voice to iPhone users "by taking advantage of advances in mobile browsers".