Last week, the Otago board voted unanimously in favour of the merger.
The Southland board was undeterred by last-minute submissions from representatives of Southland senior doctors and nurses.
The merger now requires only Health Minister Tony Ryall's seal of approval to proceed.
The exact timing of Mr Ryall's decision remains unclear.
The minister yesterday said he would need to receive formal advice from the boards, consider the matter, and make a recommendation to the Cabinet within the next month.
However, the boards, which want the new board elected in October, have said they were expecting Mr Ryall to make a decision by February 18.
Otago chairman Errol Millar said yesterday's decision was "only the end of the beginning, rather than the beginning of the end". Mr Millar was in the public gallery at the Southland meeting for the discussion, which lasted less than an hour.
He said if the minister's decision agreed with the boards', it would mean the start of much hard work to ensure a thorough change-management process in which staff were closely involved.
Chief executive Brian Rousseau responded to criticism about a lack of information on how the merger would work in practice, and to concerns about sustainability of services in Southland Hospital.
He said such issues would be best addressed by clinicians from both regions "getting together and thrashing out an agreement" to see how the hospital should be supported.
"That cannot be done in a vacuum," he said.
In response to concern about the consultation process, the board had sought a legal opinion from Anderson Lloyd, which said the process appeared to have been sound and pretty thorough, Mr Rousseau said.
At the instigation of chairman Paul Menzies, members voted unanimously that dual Otago-Southland board members, ministerial appointees Tahu Potiki and Susie Johnstone, should have full voting and speaking rights.
This followed the senior doctors' suggestion they should consider their potential conflict and abstain.
Both spoke in favour of the merger, as they had at the Otago meeting, with Mr Potiki saying there were more than 10 solid initiatives by the boards to improve clinical and financial sustainability which were at the point of being frustrated by the two-board situation.
Mrs Johnstone, who is the deputy chairwoman of both boards, said it was wrong for people to assume that board members took an adversarial approach to everything and only represented the area from which they came.
The motion in favour of the merger was moved by Fiona McArthur, who said she was happy to run the risk of making herself redundant.
Mr Menzies seconded it.
Others who voted for the motion were Katie O'Connor, Sajan Bhatia, and Tim Ward. Neville Cook was absent.
Kaye Crowther, Karen Goffe and Dot Wilson voted against the merger.
Mrs Crowther said she believed there was a political agenda to the merger and the Government should be honest with the public.
The board was trying to do too much with many projects, such as the reduction in spending on the elderly and the hospital capacity review, she said.
Ms Goffe said effective change was driven from the bottom up, not the top down. and more effort needed to be put into involving the "nuts and bolts" of the organisation.
Speaking after the meeting, the senior doctors' representative, Dr Charles Luecker, said the group would meet today to consider what it might do next.
It was likely to involve ensuring Mr Ryall knew of its concerns.
