Viviendi said on Sunday it would buy the site for $5 per share in a cash and stock deal valued at about $372m.
The move comes eight months after Vivendi successfully sued MP3.com over copyright violation.
Vivendi was one of five major record companies to sue MP3.com - and the only one that refused to settle before the case reached court.
Vivendi hopes this latest move will help advance its efforts to create an online digital music subscription service - and reach 40 million registered internet users.
Michael Robertson, MP3.com chairman and chief executive officer, said the online company would continue its own services while developing new offerings with Vivendi.
Duet
"MP3.com will be a great asset to Vivendi Universal in meeting our goal of becoming the leading online music service provider," said Jean-Marie Messier, chairman and chief executive officer of Vivendi Universal.
MP3.com will be a likely candidate for Vivendi Universal's Duet, an online digital music subscription service it is developing jointly with Sony, said Anita Larsen, a spokeswoman for Vivendi.
The Duet service is expected to launch this summer, streaming music online and planning to offer music downloads.
Vivendi said it would have thousands of songs on the internet from Universal Music Group, a subsidiary, and Sony Music Entertainment available in a fee-based subscription model.
Details about how the service will work and how much it will cost have not been announced.
Approved
Vivendi said MP3.com's board unanimously approved the deal, and that holders of more than 50 % of MP3.com's outstanding shares would vote in favour of the sale.
"The transaction has been structured as a reorganisation that will be tax free to MP3.com shareholders to the extent they receive Vivendi Universal shares," the company said in a news release.
In September, a federal court judge in New York ruled that MP3.com had intentionally violated the copyrights of the music companies, and awarded Universal Music Group penalties that could have reached as much as $250m.
Two months later MP3.com agreed to pay the company $53.4m.
Vivendi Universal owns Universal Music Group and Universal Studios, a 51% stake in European pay-TV provider Canal, and other holdings.