Prosecutors in the troubled Cabinda province where the shooting took place said two members of the Front for the Liberation of the Enclave of Cabinda forces, or Flec, were captured on Sunday.
Several Togo players were injured in the attack, some of them seriously.
Reserve goalkeeper Kodjovi Obilale, who was shot twice, is in a stable condition in intensive care in a South African hospital after undergoing emergency surgery.
"The medical team is satisfied with the progress of Mr Obilale," said doctor Ken Boffard. "He will however remain in the trauma intensive care unit until he is fully out of danger."
Boffard stated that one of the bullets that hit Obilale would not be removed from his body because of the risk of causing further injury.
During the tournament's opening ceremony in Luanda on Sunday, Angolan President Jose Eduardo dos Santos condemned the attack but insisted that Cabinda would still play a part in staging the event.
"Despite the terrorist attack, Cabinda will remain a hosting city," he said. "There is no need to be afraid."
The first match took place in Cabinda on Monday with Ivory Coast playing Burkina Faso. There are another three games due to be played there: Ivory Coast v Ghana, Mali v Malawi and one of the quarter finals on 24 January.
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