Beddau and Bonymaen have failed to reverse the decision which denied them promotion to the Welsh Premiership.
The League One East and West champions lost a vote at Sunday's Extraordinary General Meeting in Port Talbot, with 67% of clubs voting against them.
The clubs were denied promotion after failing to meet the Welsh Rugby Union's ground criteria for Premiership clubs.
But they argued the WRU changed the rules mid-season, denying them time to make the necessary improvements.
WRU group chief executive Roger Lewis said: "We fully recognised the emotional arguments for Beddau and Bonymaen because they have achieved so much on the field of play, but the rules of governance have to be obeyed.
"Beddau and Bonymaen are important clubs with proud histories and we applaud and honour them for that.
"The consequences of bending to the emotion of their arguments would not have been acceptable and, furthermore, would have damaged our image as a rugby nation."
In July 2006, the WRU informed all Division One club they had until June 2007 to "show substantial progress to achieving the required Premiership Entry Criteria and any extra time needed to complete all works before the 2007/08 season starts".
But in September last year, that deadline was brought forward to January 2007.
Beddau and Bonymaen argued that gave them far too little time to complete improvements to their facilities and asked for the original deadline to be reinstated.
But only 33% of the 320 delegates at the Princess Royal Theatre in Sunday's EGM supported their motion, condemning both clubs to another season in Division One.
The clubs needed a 75% majority to defeat the WRU.
This is the second time in 12 months that the WRU has faced an EGM from its member clubs.
The governing body survived a vote of no confidence following the dismissal of Mike Ruddock as Wales coach, but it was defeated over its failure to appoint a group chief executive.
That led to the eventual appointment of Roger Lewis, who argued the WRU's case against Beddau and Bonymaen on Sunday.