Former Vice President Saulos Chilima and nine others were killed when the military plane they were travelling in crashed in a forest on June 10.
Chilima was expected to challenge Chakwera in next year's presidential election.
Usi will be sworn into office this Friday, a government statement said.
He previously served as Minister of Natural Resources and Climate Change and is a close ally of Chilima having served as his running mate.
--Reuters--