Health Secretary Jeane Freeman said today this was the only way to ensure standards are maintained at the Home Farm care home on the island.
The £900,000 purchase of the facility from HC-One was funded by the Scottish Government, but it is unclear whether the firm stands to profit from the purchase.
Ms Freeman said the move will secure the "well-being" of residents in the home.
"We have worked closely with NHS Highland and the Care Inspectorate to secure this," Ms Freeman said.
"Significant improvements have been made in quality of care offered at Home Farm, with support from the Healtrh board the Care Inspectorate, the local council and the staff there."
She added: "The future ownership of Home Farm by NHS Highland also provides and assurance for people on the island that provision of residential and nursing care in their community will continue."
All staff working at the home will now be transferred to NHS Highland.
A total 30 residents and 29 staff tested positive for Covid-19 at the home during the outbreak.
The Care Inspectorate took legal action to have HC-One removed as the main provider of care to residents followed an unannounced inspection of the home in May that raised "serious concerns" about the quality of care.
The action was dropped last month following improvements in care.
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