The intellectual property lawsuit was filed in a California yesterday (12 March). The patents in question related to methods and systems for advertising and payments on the web.
Until now, the "patent wars" have largely been related to hardware companies such as Apple, Motorola and Samsung.
However, they are now being fought on multiple fronts and, at the end of last year, BT announced it was suing Google over claims it had infringed copyright on several BT products.
The lawsuit comes at a sensitive time for Facebook as it prepares to go public in what is expected to be the largest internet IPO in history.
Yahoo declined to comment, but a Facebook spokeswoman said: "We're disappointed that Yahoo, a long-time business partner of Facebook and a company that has substantially benefited from its association with Facebook, has decided to resort to litigation.
Alluding to previous reports that Yahoo was preparing to sue, the spokeswoman said: "Once again, we learned of Yahoo's decision simultaneously with the media. We will defend ourselves vigorously against these puzzling actions."
Yahoo and Facebook have worked in partnership in the past, and in , talked up this relationship, prior to the news hitting the headlines.
A report by Reuters claimed the move could be due to Yahoo trying to boost its acquisition value.
It is the first major move by newly installed Yahoo chief executive Scott Thompson.
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See this week's Marketing magazine for an analysis on the ongoing patent wars.
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