A Togolese minister said the government had decided to pull the team out of the tournament because of "this dramatic situation", but Ivory Coast and Ghana confirmed they would take part.
Seven members of Togo's delegation were wounded and the bus driver was killed in Friday's attack in the province of Cabinda. It was claimed by the FLEC, a rebel group that has been fighting for secession sporadically for decades.
It was the second militant attack on an international sports team in less than a year. Last March, six policemen and a driver were killed when gunmen attacked a bus carrying Sri Lanka's cricket team in Pakistan.
The assault raised questions about security for the World Cup taking place in South Africa in June, but organisers of that event said it was 'nonsensical' to draw comparisons.
Togolese officials named the dead men as media officer Stanislas Ocloo and assistant coach Amalete Abalo, and said reserve goalkeeper Kodjovi Obilale had been evacuated to Johannesburg for medical treatment.
Obilale was rushed to Milpark hospital for surgery, and hospital spokesman Barry Bedford said: "He is going into theatre now, but he is in a stable condition."
In the Togolese capital Lome, Territorial Administration Minister Pascal Bodjona said the government had decided to recall the team. "We could not continue the African Nations Cup in this dramatic situation," he said in a statement.
"This was necessary because our players are in a state of shock and because we do not think the security which should have been placed around our players is giving the necessary guarantees."
Togo's captain and star striker Emmanuel Adebayor, who escaped the attack badly shaken but unharmed, was already flying home, his English club Manchester City said.
BUS TRAVEL BANNED
The team bus, travelling from its training ground in the Congo Republic, had just entered Cabinda, geographically cut off from the rest of Angola, on Friday when it came under fire.
"I know I am really lucky," said midfielder Moustapha Salifou. "A defender who was sat in front of me took two shots in the back.
"Our security people saved us ... They were in two separate cars, about 10 of them in total, and they returned fire. The shooting lasted for half an hour and I could hear the bullets whistling past me. It was like a movie."
Virgilio Santos, an official with the African Nations Cup local organising committee COCAN, said teams had been told explicitly not to travel to the tournament by road.
"We asked that all delegations inform us when they would arrive and provide the passport number of their players," he told the sports weekly A Bola.
"Togo was the only team not to respond and did not inform COCAN it was coming by bus ... The rules are clear: no team should travel by bus. I don't know what led them to do this."
Organisers said on Friday the tournament would start as planned on Sunday.
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