Confirming recent speculation, the US firm said the 13-year-old WLM service will end in March 2013, except in China.
This means that millions of Messenger users will instead reach their friends and contacts through Skype, the internet telephony business that Microsoft acquired last year for $8.5 billion.
WLM launched in 1999 as MSN Messenger, and grew to around 330 million active users worldwide ten years later, as well as adding video calls, photos and games to its text-based service.
It is currently understood to have around 8.3m unique users in the US, although its audience has been declining in recent years.
"Our goal remains to deliver the best communications experience for everyone, everywhere. We want to focus our efforts on making things simpler for our users while continuously improving the overall experience," said Microsoft in a statement.
This forms part of Microsoft's strategy to integrate Skype more across its services, including the recent Skype 6.0 for Mac and Windows, which allows users to sign in using a Microsoft or Facebook account.
Messenger users can now update to the latest version of Skype, sign in with their Microsoft account, and then all their existing Messenger contacts will be there, said Microsoft.
They will also be able to access other features, such as broader device support for all platforms, including iPad and Android tablets, along with instant messaging, group video calling, and calls to mobile and landlines.
But there has been no indication as to whether the WLM games will also be available through Skype.
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"We will work with you over the next few months to help you transition and offer information and help along the way. To help you learn how to get the most out of Skype, be on the lookout for some special offers later this year as you join your Messenger friends in the migration," Microsoft said.
"We think you will enjoy using Skype, and encourage you to download the latest version, sign in with your Microsoft account, and experience it for yourself."
Microsoft is taking a risk by canning WLM, because it still has more than double the users of Skype's own instant-messaging tool, according to comScore data.
There is a danger that Microsoft could push people to rival services, such as Yahoo Messenger, WhatsApp, or Google Talk, but the firm will no doubt hope that the strength of its new Skype service will keep people loyal.