Permission to appeal has also been refused.
The WRU's planned reforms of the Principality Premiership and the establishment of a new 14 club National Championship Division will now be implemented.
The announcement of the Welsh rugby league structures and fixtures, which has been delayed pending the outcome of the legal proceedings brought by Pontypool, will now go ahead as soon as possible.
The Group Chief Executive of the WRU, Roger Lewis, said: "We can now all place this issue behind us and move forward in the best interests of Welsh rugby.
"We were disappointed that Pontypool decided to take this legal action against the Union. We cannot achieve change without facing up to difficult decisions. It is important we all now move on in harmony for the sake of the game.
"The WRU encourages the coaches, administrators and supporters of Pontypool to seize the opportunity we have created with the new National Championship Division to make the progress they seek as a club.
"Pontypool RFC has a proud place in Welsh rugby and we are confident that the supporters and the team will embrace the challenges of the new season with their usual energy and enthusiasm."