The new deal will bring an annual 8.7 million pounds to the regions to be spent on players qualified to represent Wales.
The disagreement had left Wales captain Sam Warburton in limbo after he signed a central contract before the regions, including his club Cardiff, said they would not select players on centrally-funded deals.
New selection rules mean players based outside Wales will not be eligible for the national team, although coach Warren Gatland can make exceptions. Players who are already based overseas are exempt from the regulation.
"The new contracts will help us keep more of our best players in Wales and will help stem the flow abroad of the talent we develop here through our academies and regions," WRU chief executive Roger Lewis said in a statement.
(Reporting by Josh Reich, editing by Ed Osmond)
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