The series' commercial rights holder Dorna has signed a four-year deal with the Italian company, which will provide, on demand, an engine and chassis control unit with all relevant tuning and data analysis tools.
While the spec ECU will be optional - teams will still be able to use their own custom-designed ECUs at their own discretion - the announcement comes in the wider context of Dorna's push for a single control ECU to be made mandatory within the next few years.
Electronics have come to play an increasingly central role in MotoGP, especially due to the fight to extract the maximum performance from just the 21 litres of fuel permitted for prototype bikes.
Dorna believes a spec ECU would bring down costs and improve the racing, although there remains resistance from the factories.
CEO Carmelo Ezpeleta hailed the deal with Magneti Marelli - which will include assistance at every circuit and continual development across the year - as a significant step for the championship.
"I cannot hide the fact that I am very happy with this new cooperation with Magneti Marelli," he said.
"The agreement reached we have reached with the Italian company merely validates MotoGP as a competition that incorporates and encourages the latest and most innovative technology.
"The experience of this company, which has spent many years at the highest level of competition in motor sport, represents a major step in the premier-class of two-wheel racing."
Robert Dalla, Magnetti Marelli's motorsport managing director, said his chief objective was to reduce the costs of such high-end technology.
"The main aim is to provide top technology at affordable costs, which is Magneti Marelli's mission firstly in racing and also in the field of series production," he said.
"We are very glad to share our know-how and experience in the motorsport field with MotoGP, in order to jointly achieve new objectives in terms of performance and technology development.
"This new initiative with Dorna represents a further strategic opportunity to enhance the development of our technology."
Honda has been one of the staunchest advocates of independent electronics, and has previously said that it could switch focus to the rival World Superbike Championship should spec ECUs become mandatory in MotoGP.
- Magneti Marelli