Bee editor-in-chief Kyle Mann initially alerted fans that Twitter had taken action against the outlet's account.
"Your account, TheBabylonBee has been suspended for violating the Twitter Rules. Specifically for: Violating our rules against platform manipulation and spam," Twitter wrote in an e-mail posted by Mann. "You may not use Twitter's services in a manner intended to artificially amplify or suppress information or engage in behavior that manipulates or disrupt's people's experience on Twitter."
The suspension sparked a major outcry among conservatives who launched a #FreeTheBee campaign on Twitter.
Less than an hour later, the Bee's account had been restored.
CEO Seth Dillon published another email from Twitter about the "mistake" it had made.
"We're writing to let you know that we've suspended your account. We're sorry for the inconvenience and hope to see you back on Twitter soon," Twitter wrote. "We have systems that find and remove multiple automated spam accounts in bulk, and yours was flagged as spam by mistake. Please note that it may take an hour or so for your follower and following numbers to return to normal."
A spokesperson for Twitter told Fox News, "This account was mistakenly caught in a spam filter. This has been reversed and the account has been reinstated."
The Babylon Bee, which is widely seen as a conservative alternative to "The Onion," was founded in 2016. It describes itself as "Christian News Satire" and has become known for lampooning Democratic politicians and liberal media outlets.
Earlier this year, the Bee had some fun at the expense of CNN after one of its reporters accused the outlet of spreading misinformation.
"CNN Attacks Babylon Bee: 'The Internet is Only Big Enough For One Fake News Site,'" the Bee's headline read.