MotoGP will adopt a control ECU for all entrants from 2016, bringing an end to its current two-tier structure.
The debate over the future of MotoGP electronics has been a fierce one, with current champion team Honda threatening to walk away from the championship if series-issued systems were mandated.
But at a meeting of the Grand Prix Commission - on which Honda and fellow works team Yamaha are represented by the Motorcycle Sports Manufacturers' Association - in Qatar on Tuesday, it was agreed that a control ECU would be brought in after two more years.
Honda, Yamaha and all "current and prospective participants" will be able to assist with the design and development of the new software.
Ducati had drawn the ire of Honda by helping to develop Magneti Marelli's spec system over the 2013/14 winter, before announcing it would use that software and run in the Open class.
"The championship ECU and software will be mandatory for all entries with effect from 2016," said a commission statement.
"During the development of the software a closed user web site will be set up to enable participants to monitor software development and to input their suggested modifications."
MotoGP has also adjusted the regulations for its current Factory and Open class split.
The latter category was intended as a lower-cost option for independent teams running the standard ECU.
Open runners get 24 litres of fuel per race compared to Factory bikes' 20 and are allowed 12 engines per year rather than five, with the engine freeze waived.
Now the GP Commission has announced that any manufacturer with a Factory entry that has not won a dry race in preceding season, automatically gets the same benefits as Open entries, meaning Ducati's switch was ultimately unnecessary as it has not won since 2010 so is entitled to the breaks.
Suzuki, which will rejoin the series in 2015, is set to get the same allowance.
But those concessions can be removed if a team achieves a set level of success, as had been proposed in the 'Factory 2' tier outlined by MotoGP commercial chief Carmelo Ezpeleta last week.
If a manufacturer with those benefits wins a race, gets two second places or three podium finishes in the dry, its fuel allowance will be brought down to 22 litres.
Three wins would mean it loses the use of the softer tyres provided to Open entrants.