Bondo was sent home midway through last year's tournament after his questionable handling of the Zimbabwe/Madagascar tie.
The Zimbabwe officials lodged a complaint with the COSAFA Referees Committee, after claiming their team was denied two clear cut penalties.
"Every year, COSAFA makes its independent selection of referees that will given responsibilities at the annual regional tournament. This year, Botswana is fortunate again to have top referee in Tirelo Mositwane as part of the selected officials," Botswana Football Association (BFA) spokesperson, Tumo Mpatane said.
(Seychelles), Ahmad Imtehaz Heeralall (Mauritius), Jackson Pavaza (Namibia), Hamada Nampiandraza (Madagascar), Mositwane (Botswana and Celso Alvacao (Mozambique).
There are also nine assistant referees who include James Emile (Seychelles), Souru Phatsonae (Lesotho), Athenkosi Ndongeni (South Africa), Sifiso Nxumalo (Swaziland), Matheus Kanyanga (Namibia), Romeoe Kasengele (Zambia), Fabian Cauvelet (Mauritius), Clemence Kanduku (Malawi) and Mmadi Faissoil (Comoros).
The COSAFA Cup will run from May 27 to June 9. The Zebras are leaving on Friday for South Africa.
Their first match is against Angola is on Monday. Zimbabwe are the defending champions after defeating neighbours, Zambia 3-1 in the final at the Royal Bafokeng Sports Palace last year.