The move follows the launch of the designated WhatsApp Business app in January.
The new platform will allow brands to reply to users who contact them and send notifications such as shipping confirmations, appointment reminders or event tickets. Replies sent within 24 hours of the original message will be free, with those sent after 24 hours charged.
The mechanism means that brands will be financially rewarded by Facebook by providing fast customer service.
Facebook said in a blog it was already using the platform with brands including Uber, Wish and Singapore Airlines.
The tech company is also offering ads in Facebook that click to a pre-filled WhatsApp chat, with advertisers using this getting two new metrics in Facebook Ads Manager: conversations started and messaging replies.
The messaging fees will account the first revenue of any kind that WhatsApp has generated for Facebook since the platform abolished its $1/£0.99 subscription fee in 2016.
Warren Levitan, chief executive at Smooch - a conversation platform that connects business software to various messaging channels - said: "Across our customer base consisting of thousands of brands who are actively messaging their customers, there is absolutely no channel that has been more in-demand than WhatsApp.
"On one level it's about the app's security and privacy — more than ever, brands are sensitive to their customer interactions being mined for competitor insights, and no business messenger is as secure and trustworthy as WhatsApp."