Marussia, the smallest team in the sport, went into administration at the end of last season and survived only after a late rescue deal was put together. They have used Ferrari engines for the past two years.
The new partnership comes amid a general shakeup of the engine landscape, with Renault set to buy Mercedes-powered Lotus and Red Bull's two teams negotiating with Ferrari after breaking from Renault.
Champions Mercedes, whose engine is the most competitive in the sport, said the deal with Manor was a multi-year one and the units provided would be 'current year'.
"This new agreement should enable us to keep our supply roster at three customer teams for 2016, which is our ideal level in terms of technical and logistical capacity," said Mercedes High Performance Powertrains director Andy Cowell.
"We will be targeting gains in both performance and reliability for the 2016 Power Unit and look forward to delivering those to our new customers at Manor Marussia F1 Team."
Mercedes also provide engines to Force India and former champions Williams as well as the works team of Lewis Hamilton and Nico Rosberg but have baulked at supplying arch-rivals Red Bull.
Marussia principal John Booth said his team would resume a previous technical partnership with Williams Advanced Engineering for the supply of transmission and suspension components.
"Combined with Mercedes-Benz Power Units, we are very excited about the strength of our new powertrain package and what it means for the long-term future of our team," he said.
Marussia have scored no points this season, after taking two last year with the late French driver Jules Bianchi in Monaco. Their drivers this season have been Britain's Will Stevens, American Alexander Rossi and Spain's Roberto Merhi.
The 2014 points secured ninth place in the championship, ahead of Sauber and now-defunct Caterham, and prize money that has been crucial to the team's survival.
"Together with the potential we are seeing with our 2016 car in the wind tunnel, the Mercedes-Benz Power Unit will assist our return to aggressive performance development with effect from next season," said Booth.
(Reporting by Alan Baldwin, editing by Amlan Chakraborty)
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