The Victorian Rugby Union and players' association called the meeting last month and tabled a resolution to reconsider the cull, which the ARU had agreed as part of the competition's contraction from 18 teams to 15 next year.
ARU chairman Cameron Clyne said members had voted down the resolution at the EGM.
"The majority of members have voted in support of going from five teams to four," Clyne told reporters at ARU headquarters in Sydney.
With New South Wales and Queensland states holding six of the 15 votes, and set to gain from the axing of one of the country's five Super Rugby teams, there was little prospect of the resolution carrying.
Clyne said a separate motion to set up a Super Rugby commission had passed, however.
The motion was criticised by local pundits for proposing an advisory body to the ARU as opposed to an independent entity that could wield executive power.
"We've had that commission in the past so we're very comfortable to have that discussion and work out as to whether we do establish that in the future," Clyne said.
ARU chief executive Bill Pulver, who has been under fire over the governing body's handling of the Super Rugby cull, said at the weekend he would resign at the EGM if called upon by members.
But there was no no-confidence vote put forward and he will remain in the role.
South Africa agreed to cut two teams from Super Rugby and are expected to announce that the Southern Kings and Bloemfontein-based Cheetahs will be axed at a meeting on July 7.
The ARU have set no timeframe and are battling legal challenges from both the Rebels and the Perth-based Force over the cull.
Super Rugby expanded from 15 teams last year with the addition of new franchises from Argentina and Japan, and the return of South Africa's Kings.
But the re-jigged competition fell flat with fans, broadcasters and media pundits, who felt the expansion had lowered the quality of games and turned away viewers.
(Writing by Ian Ransom; Editing by John O'Brien)
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