A South African Airways flight was not allowed to take off from Zim-bob-we's Harare airport for a trip to Johannesburg on Saturday.
Another flight from Johannesburg to Harare was also cancelled.
Authorities in Zim-bob-we said the planes were blocked for failing to comply with civil aviation rules.
The move follows the grounding of an Air Zim-bob-we flight at Johannesburg's main international airport on Friday.
Both countries said they imposed restrictions because the planes did not have a "foreign operator's permit".
A South African Airways front man said officials had asked to see certain documents that had not been requested in two decades.
Allegations against Grace Mugabe
The tit-for-tat between the two countries comes as Zim-bob-we's first lady, Grace Mugabe, faces allegations of assaulting a young South African female model at a luxury hotel in Johannesburg.
Twenty-year-old Gabriella Engels has accused Grace Mugabe of barging into a hotel room where Engels was waiting to meet one of Mugabe's sons on Sunday and whipping her with an extension cord.
South African police issued a "red alert" on Friday at the country's borders to prevent Mugabe from fleeing undetected.
Her whereabouts were not known on Friday, but South African police minister Fikile Mbalula said she remained in the country.
The 52-year-old, who has not yet been charged, has asked for diplomatic immunity in the case.
Lawyers for Engels have threatened to go to court if immunity is granted.
It is not clear whether Mugabe entered South Africa on a personal or diplomatic passport.
South Africa's government said it had not yet decided whether to grant the request for diplomatic immunity.
South Africa grants Grace Mugabe diplomatic immunity[Guardian] South Africa has granted diplomatic immunity to Zim-bob-we’s first lady, Grace Mugabe, allowing her to avoid prosecution for the alleged assault of a 20-year-old model, a security source has said.
Despite confusion about Mrs Mugabe’s whereabouts, South African police said she was still in the country.