Previously, NPB teams had taken blind bids from MLB teams on players made available before deciding whether to accept a bid that would allow that MLB team a 30-day window to negotiate a contract with the player.
The new accord will bring more major league teams into competition for incoming Japanese league players and could shift some of the rewards from the NPB clubs to players themselves.
The Texas Rangers offered a record posting fee of over $51 million in 2011 for Nippon Ham Fighters pitcher Yu Darvish, who joined the AL West team after signing a six-year, $60 million deal.
The posting fee for Darvish was slightly higher than one paid by the Red Sox five years earlier for Daisuke Matsuzaka, who signed a six-year deal with Boston for $52 million.
"We are pleased to have amicably reached an agreement that addresses various issues raised by all parties," MLB Chief Operating Officer Rob Manfred said in a statement.
"Major League Baseball values its longstanding professional relationship with Nippon Professional Baseball, and we look forward to continuing the growth of the great game we share in the years to come."
Highly prized pitcher Masahiro Tanaka, 25, of the Rakuten Golden Eagles may be the first major player affected.
Tanaka, who went 24-0 with Rakuten last season, may hit a bigger-than-expected jackpot due to the new protocols or not be posted this year because of the imposed ceiling.
Under the agreement, an NPB club making one of its players available would notify MLB and set a "release fee" that a major league club would have to pay for a player's release.
The NPB club may not set the release fee higher than $20 million and the fee cannot be changed once it has been set by the NPB club, under the new agreement.
MLB would notify all its teams of an NPB player's availability and the release fee set by the NPB club.
All postings of NPB players would have to made between Nov. 1 and Feb. 1, with MLB teams having 30 days to reach a contract agreement with the player.
An MLB team signing the player would pay the Japanese club the designated release fee in a series of installments.
Any posted NPB player who fails to reach an agreement with a major league team would remain under reserve to his NPB club and no release fee would be owed.
The new posting agreement will be in place for a period of three years, continuing year to year afterwards until either MLB or NPB decides to terminate the agreement.