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Mohammed Kalim and Firoza Begum were told about their new resident status on Wednesday.
MPs and lawyers had been fighting for the couple since a clerical error in processing their most recent annual working visas led to her receiving an order to be deported back to Fiji.
In 2007, Mr Kalim began work as a halal butcher at the Finegand processing plant and Mrs Begum worked at New World Balclutha until 2016, when she had a severe stroke that left her in a wheelchair.
Mr Kalim said he was "excited" by the department’s change of heart.
"I’m feeling very good. A lot of relief. It was very stressful and I was worried for her."
He wanted to thank Clutha-Southland MP Hamish Walker, New Zealand First list MP Mark Patterson and Geoff Mirkin, of Wilkinson Rodgers Lawyers, for their help.
He also wanted to thank the Otago Daily Times, which alerted others to their plight in a report in July.
Mr Mirkin said he and associate Werner van Harselaar, who worked pro bono on the case, wanted to argue it on humanitarian grounds to the Immigration and Protection Tribunal but they were outside the 42-day appeal period after the application was declined.
After lobbying, Associate Immigration Minister Poto Williams intervened and temporarily halted her deportation and indicated the couple would be granted residency if they met requirements.
"We spent the last three months helping them meet all the requirements. Last night we had in our hot hands two residency certificates," Mr Mirkin said.
Mr Walker said there had been "heartbreak" over the uncertainty as "he’s a very respected member of the freezing works down there. They contribute to the community and are very well respected."
"It’s a huge turnaround. It just shows what a little bit of pressure can do."
A spokesman said Ms Williams did not comment on individual immigration cases and Immigration New Zealand was unable to respond about the case yesterday.