The Angop news agency said the two suspects were arrested in the province of Cabinda where the machine-gun attack took place Friday, two days before the Africa Cup of Nations.
The separatist Front for the Liberation of the Enclave of Cabinda (FLEC) claimed responsibility for the attack and threatened further attacks during the football tournament, which runs until the end of the month.
Togo's national football team flew home on Sunday from Angola after pulling out of the tournament.
The opening game of the Africa Cup of Nations between hosts Angola and Mali went ahead on Sunday in the capital Luanda while Cabinda is scheduled to host its first match later Monday when Ivory Coast take on Burkina Faso.
Although the match between Togo and Ghana has been called off, there have been suggestions that the Togo team could return to play its other matches at the end of the three days of national mourning declared in honour of the victims.
The bus driver, assistant coach Abalo Amnalete and team spokesman Stanislas Ocloo died in the attack. Goalkeeper Kodjovi Obilale was airlifted to an intensive care unit in South Africa to receive treatment for gunshot wounds.
Officials at Johannesburg's Milpark hospital said on Monday that the medical team treating Obilale was "satisfied" with his progress.
"He will however remain in the trauma intensive care unit until he is fully out of danger," Professor Ken Boffard of the hospital's specialized trauma team was quoted as saying by South African Press Association.