Only four club representatives voted to oust the regime after WRU's former Chief Executive David Moffett prompted the vote.
The four Welsh regions have denied any agreement that Wales Captain Sam Warburton will be guaranteed to play regional rugby next season.
Former Wales player Rhys Williams has expressed his concern that players will be "used as pawns in tactical chess game" in on-going row.
Wales team v @bokrugby Forwards: G Jenkins, K Owens, S Lee, L Charteris, A W Jones (Capt), D Lydiate, J Turnbull, T Faletau (2/3)
Wales team v @bokrugby Bench: M Rees, P James, A Jarvis, J Ball, D Baker, G Davies, J Hook, M Morgan (3/3)
"Through the past six months, the Welsh Rugby Union has retained its dignity" said WRU Chief Executive Roger Lewis.
"We have not been dragged into the gutter to exchange playground insults with others."
"It's been a dark day, instigated by a very very small minority of people, and the reason I emphasise that, hundreds and hundreds of men and women supported the Welsh rugby union today" he said.
"We only had four people against us in that vote of no confidence, and the rest, hundreds, supported the Union, and that is the true reflection of where we are in Wales today."
The Welsh Rugby Union has seen off a vote of no confidence following an Extraordinary General Meeting in Port Talbot today.
Two resolutions voted on were that the WRU board of directors had not been acting in the best interests of Welsh rugby, while a second had called for a vote of no confidence in the current board.
A total of 39 WRU member clubs and Wales' four professional regions had supported calls for an EGM - the WRU's first since 2007 - with the protest driven by former chief exec David Moffett.
Moffett gained sufficient backing for the meeting to be called, but it ended after almost four hours of debate.
Disaffected clubs had claimed the WRU board of directors weren't overseeing Welsh rugby with the best interests of the game at heart.
The WRU has agreed to hold a ballot of all clubs to reach an agreement on whether a proposed new national league structure of the amateur game will go ahead, or whether the existing structure will be kept for next season.
The Welsh Rugby Union's Extraordinary General Meeting is underway in Port Talbot.
43 clubs including the four professional regions have called for the meeting to discuss concerns over league structure and WRU finances.
Ex-WRU chief David Moffett is seeking election to the governing body.
A no confidence vote at an EGM could force out elected members.
Bristol bound fly-half Matthew Morgan has described his surprise selection for Wales' tour to South Africa as a 'dream come true'.
Morgan was overjoyed to be selected in Warren Gatland's 32 man squad after an impressive cameo off the bench for the Possible during their defeat at the hands of the Probables at the Liberty Stadium last night.
Gatland was full of praise for the 21 year-old saying he 'came from nowhere' to force his way into the New Zealanders plans. Wales fly out for their two test tour on Thursday.
Wales Squad to South Africa:
L Williams, M Morgan, J Williams, G North, A Cuthbert, C Allen, J Roberts, J Davies, S Shingler, J Hook, D Biggar, M Phillips, R Williams, G Davies.
G Jenkins, P James, A Jones, R Jones, S Lee, A Jarvis, K Owens, M Rees, S Baldwin, A-W Jones (Captain), L Charteris, J Ball, I Evans, A Shingler, J Turnbull, D Lydiate, T Faletau, D Baker.
Rob Howley and Robin McBryde have named their sides for Friday's Probables v Possibles senior trial.
England-based players including Gavin Henson, Paul James and George North miss out, leaving Henson's hopes of a Wales return looking slim.
The Probables versus Possibles Wales rugby trials will return after a 14-year absence this summer, the WRU has announced.
The match will be played at Swansea's Liberty Stadium on Friday 30 May and will be a chance for players to impress ahead of selection for the upcoming tour to South Africa.
Warren Gatland says it will also act as important preparation ahead of next year's Rugby World Cup.
The WRU says a survey shows more than half the population of Wales is involved with rugby as a player, supporter or follower of broadcast and newspaper coverage.
It also says 41% of the adult population in Wales have been to the Millennium Stadium to cheer on Wales and 30% (equivalent to 732,000 people) told researchers they would attend a match in the future.
The Union commissioned the eightyone600 survey as a benchmark to help it understand the position rugby has in Wales.
Price is the major factor of influence when it comes to supporters deciding to attend matches, with half saying the cost of attending is their biggest consideration when preparing to buy.
The WRU says the full detail in the survey will be used to steer its strategy to enhance the relationship member clubs and fans in general have with the game in Wales.
Rugby Champions Cup - replaces Heineken Cup. 20 teams: 6 English and French clubs, 7 from Pro 12 including best placed side from Wales, Scotland, Ireland and Italy. Final place decided by England/France playoff.
Challenge Cup - 20 teams, including 18 from Pro 12, Premiership and Top 14 + 2 other countries.
Qualifying Competition - 12-18 teams from developing nations and Italy
NEW MANAGING BODY:
European Professional Club Rugby (EPCR). Replaces ERC
An extra £1m a year for Welsh regions
Competition funding split equally between member leagues
SHARED BROADCASTING RIGHTS:
Sky and BT to show joint coverage of European competitions