Amathole District Municipality Mayor Khanyile Maneli's wife, Matilda Beauty Nontsapho Maneli, 58, has died of Covid-19.
She died at Stutterheim Hospital at 08.30 on Saturday, said family spokesperson Sithembele Zuka.
Zuka added the mayor's results came back negative on Saturday after he took a test on Monday.
He had been in self-isolation pending the results.
Amathole, with a seat in East London, is one of the largest district municipalities in the Eastern Cape.
Zuka said: "The executive mayor is deeply shocked by the passing of his dearest wife, but he's also strong and determined to fight the pandemic. He is also relieved by the fact that his test results came back negative today."
Council speaker Nonceba Ndikinda expressed sadness over Matilda's death.
"On behalf of the council and the entire municipality family, I would like to express our heartfelt condolences to the executive mayor and his entire family. We plead that the family be given space to process and mourn in peace," said Ndikinda.