The action places Apple among a group of major US companies who have cut ties or services to the whistle-blowing website and have subsequently been targeted by hackers sympathetic to WikiLeaks.
The $1.99 app was initially released Friday and allowed users of Apple's iPad or iPhone devices to access WikiLeaks with a single click, rather than having to use a web browser to navigate to the site.
The app has no official ties with WikiLeaks, but its developer did promise to donate all the income to the site.
"We removed the WikiLeaks App from the Apple Store because it violated our developer guidelines," said Trudy Muller, a spokeswoman for Cupertino, California-based Apple. "Apps must comply with all local laws and may not put an individual or target group in harm's way."
Apple keeps strict tabs on the apps it offers, unlike the more open platform offered on rival Android phones, prompting some users to "jailbreak" their devices to circumvent the company's restrictions.