"They are disqualified. This group (B) is a three-team tournament," Confederation of African Football (CAF) co-ordinator Yaouba Amoa told reporters on Monday.
Togo's assistant coach and media officer were killed and reserve goalkeeper Kodjovi Obilale seriously wounded by separatists from the enclave of Cabinda in Friday's attack.
Monday's Group B match between Togo and Ghana had been scheduled as the second part of a doubleheader. Burkina Faso and Ivory Coast shared a 0-0 draw in the first game at the new Chazi Stadium in Cabinda.
Togo midfielder Thomas Dossevi described the CAF decision as "ridiculous."
"It would have been simple for us to come back and play on January 21, I think Ghana would have agreed to that," he told Reuters by telephone.
"It is a serious and ridiculous decision. Everybody wanted us to be here and play the African Nations Cup."
Togo left Angola on a chartered flight sent to collect them after the attack but had expressed the hope they might be able to return and compete at the tournament.
Several players spoke of their willingness to play on but they were ordered home by Togo's government.
The CAF official said it would be impossible to change the tournament schedule.
