Factory outfits will be allowed to continue running their own software provided they also run with 20, rather than 24, litres of fuel. They will also be restricted to five engines, compared to 12 for other teams.
Promoter Dorna first announced the new regulations in November last year, but stressed that they would only come into effect should Honda and Yamaha agree to new engine and chassis supply deals.
A deadline of the opening round of 2013 was set for negotiations.
Honda, which had threatened to quit should spec systems be enforced even for factory teams, agreed to lease satellite bikes for a maximum price of 1.5 million Euros.
On Saturday Yamaha confirmed it too had reached a new agreement with Dorna.
The Japanese manufacturer will lease prototype engines to independent teams from 2014.
Dorna boss Carmelo Ezpeleta said last year that he would co-ordinate with both factories regarding overall orders, and would also act as guarantor for payments.
With Suzuki being heavily linked with a 2014 return, new factory outfits will be allowed nine engines in their first seasons.
Alongside the new regulations, governing body the FIM confirmed new testing guidelines effective from the 11 November this year, the day after MotoGP's Valencia finale.
Riders will be permitted one three-day test before November 30, and then a trio of three-day tests between February 1 and the start of the 2014 season. Three one-day tests will be permitted during the season at events specified by Dorna.