Nyondo, who scored both goals when the Flames went down 3-2, fainted after being injured by one of the missiles thrown by the home fans soon after MalawiÃ¢â‚¬â„¢s second goal.
FAM first vice-president Moses Mkandawire said the association will launch a protest.
“We are writing to CAF over the incident. Our players and technical officials were pelted with missiles by the fans and this led to Atusaye suffering a head injury.
“We expect CAF to take a stern action on Chad FA for its failure to provide security. Our players were in fear,” said Mkandawire.
But Mkandawire said Nyondo is in stable condition.
Flames coach Kinnah Phiri attributed the loss to the hostile atmosphere.
“In fact, this is not the first time they [Chad fans] have done this. It was the same when we played their team in last October,” said Kinnah.
CAF spokesperson Suleiman Habuba said the confederation will look into MalawiÃ¢â‚¬â„¢s complaint.
Last year, FAM also complained to CAF against hostile reception accorded to the Flames during the 2012 Nations Cup qualifier.