The application, called Manhattan Declaration, was a "call of Christian Conscience" that advocated "the sanctity of life, the dignity of marriage as the union of one man and one woman, and religious liberty," according to its website.
But after its October launch, the application drew criticism from around the Web.
Calling it "anti-gay" and "anti-choice," Change.org launched an online petition asking Apple to remove the application from its app store.
"Want to join the hate fest? There's an app for that!" Change.org said on its site.
The petition questioned Apple's decision to approve the application and deem it free of "objectionable content."
"Apple needs to hear from concerned people now! Let's send a strong message to Apple that supporting homophobia and efforts to restrict choice is bad business," it said.
On Monday, Change.org updated the petition to announce that Apple had apparently removed the application from its App Store after more than 7,000 Change.org members e-mailed the company in protest.
In a statement, Apple said, "We removed the Manhattan Declaration app from the App Store because it violates our developer guidelines by being offensive to large groups of people."
According to the Manhattan Declaration website, the declaration calls on Christians to "resist sexual immorality."
"We acknowledge that there are those who are disposed towards homosexual and polyamorous conduct and relationships, just as there are those who are disposed towards other forms of immoral conduct," it says.
In a message on its homepage, the drafters of the Manhattan Declaration said they were "perplexed" at Apple's decision to remove their application.
"The core drafters of the Manhattan Declaration have e-mailed Apple CEO Steve Jobs to learn why the declaration's iPhone app has been deleted from the company's site. Stay tuned as we post the letter after Jobs has received it and for Apple's response," they said.
This application is hardly the first to have stirred debate. Here are a few other iPhone applications that were too controversial for Apple's App store.
Last October, PepsiCo pulled the iPhone application AMP Up Before You Score from Apple's App store after it was deluged with criticism.
The application, which claimed to help men "score" with women, was launched to help the company promote its new AMP Energy drink.
In a statement, the company said removing the application was the "most appropriate course of action" after listening to "a variety of audiences," The Associated Press reported.
The app divided women into 24 categories, from artists and aspiring actresses to bookworms and businesswomen.
Once the user identified the kind of woman he was trying to score, the app provided "a cheatsheet on the stuff she's into, with lists, links and some surefire opening lines."
But that wasn't all. Assuming the guy got lucky, the app let him keep a "Brag List," with names, dates and other details. It also encouraged users to "flaunt it," by sharing their lists with friends via e-mail, Facebook and Twitter.