The Labour Party voted for the Bill, but it was opposed by New Zealand First and the Green Party.
The Government is taking the unprecedented step of removing the embattled health board from the 2016 local body elections and extending the commissioner regime until 2019, despite earlier promising the next election would go ahead as usual.
The New Zealand Public Health and Disability (Southern DHB) Elections Bill passed with 95 votes in support and 26 opposed.
It will now be considered by a select committee.
Invercargill-based New Zealand First MP Ria Bond said in the debate the move was an "appalling affront'' to southerners' democratic rights.
The public knew little about what the commissioner and her team was up to, and was "expected to take it on trust that they are doing a great job''.
Ms Bond warned of a "hidden agenda'' to base more services in Dunedin, and downgrade Southland Hospital.
The health funding formula did not support services in the regions, and this was the real "culprit'' in the board's woes.
"The minister wants to play this down as one election, but what this really is is another example of this Government putting all the power in the hands of a small, unelected few because it believes that it knows better than anybody else,'' she said.
Dunedin North MP David Clark told the Otago Daily Times Labour believed the commissioner's good work might be lost if a health board election was held next year.
"The minister has created a situation [by appointing a commissioner], and he now needs to deliver on it.
"I would encourage members of the public to have their say at the select committee, because this is a chance to have their democratic voices heard about where things need to go from here.''Health Minister Dr Jonathan Coleman said in the debate he had not taken the decision lightly.
"The Bill therefore impacts only one election at the Southern District Health Board and will help ensure that the next board to be appointed as part of the 2019 local body elections will begin its term on a more secure financial footing.''
The Government was spending money on Dunedin Hospital, and needed to have confidence in the health board.
"In September the Government approved $22.5million for urgent hospital maintenance, as well as upgrades to gastroenterology, audiology, and intensive care units.
"These projects will ensure that the immediate demands around delivery of services continue to be met while planning for the major redevelopment progress.''
Commissioner Kathy Grant was appointed in June when Dr Coleman sacked the board.
In normal circumstances, health boards have seven elected and four appointed members.
