Mr Phiri announced the move during an interview with SABC on June 9.
The development came amid widespread xenophobic attacks in the country.
Several Ghanaians have demanded the closure of South African-owned businesses in the West African country.
Ms Sibeko noted that she came to the evacuation centre to bid farewell to Nigerians.
The ambassador commended effective coordination of the process by the High Commission of Nigeria in Pretoria.
Mr Nwobi said that Nigerians who sought to renew their visas or stay permits could not get them on time and were often targeted for indiscriminate attacks.
According to him, the evacuation flight is expected to arrive at about 5:00 a.m. on Thursday.
Provincial commissioner, Tommy Mthombeni, told journalists that no arrest had been made and the motive for the attack had yet been known.
“We are responding to real concerns communities have about the effects that unchecked illegal immigration has on jobs and economic opportunities,” the presidency said.
President Bola Tinubu approved five evacuation flights to be operated by Nigeria’s private airline, Air Peace.
