YouTube said it had already removed 200,000 dangerous or misleading videos about the virus since February.
Facebook’s new policy is designed to stop it facing accusations of profiting from the spread of anti-vaccination messages.
The social network had previously allowed ads to express opposition to vaccines if they did not contain false claims.
It said the new rules would be enforced “over the next few days”, but some ads would still run in the meantime.
It added that it was launching a campaign to provide users information about the flu vaccine, including where to get flu shots in the US.
“Our goal is to help messages about the safety and efficacy of vaccines reach a broad group of people, while prohibiting ads with misinformation that could harm public health efforts,” the company blogged
Anti-vaccination groups will still be allowed on its platform.
Unpaid posts or comments that discourage people from getting a vaccination are also still permitted.
Earlier in the year, Facebook’s public policy manager Jason Hirsch told Reuters the company believed users should be able to express personal anti-vaccine views. He said and that more aggressive censorship could push people hesitant about vaccines towards the anti-vaccine camp.
The subsequent change is one of many that have recently been made to its free speech principles.