The death toll has now risen to three after the bus came under machine gunfire on Friday.
It was confirmed that the bus driver was killed in the attack, while reports from France claimed an assistant coach and a press officer have also died from their injuries.
There was confusion surrounding the condition of reserve team goalkeeper Kodjovi Obilale. It had been widely reported in the French media that he had died.
But a statement from his club, French team GSI Pontivy, read: "According to news given by coach Alain Le Dour and GSI Pontivy president Philippe Le Mestre, Kodjovi Obilale is not dead, despite the news reported on the internet, radio and television, and has been moved to South Africa."
Manchester City confirmed their striker Emmanuel Adebayor - the Togo captain - was returning home.
A statement on the club's official website read: "Togo has pulled out of the African Nations Cup after their team bus came under gunfire in Angola.
"City star Emmanuel Adebayor, who is captain of the Togo side, was unharmed in the ambush and he and his team-mates met this morning before deciding that they wished to pull out of the tournament.
"Their first game in the tournament had been scheduled to take place on Monday against Ghana, but they are now heading home to their families.
"Organisers have so far insisted the tournament will go ahead.
"The club is in regular contact with Emmanuel, his advisors and the English Football Association.
It has been made clear by manager Roberto Mancini and senior officials that Emmanuel will now be given as much time as he needs to recover from the horrific attack."
Midfielder Alaixys Romao confirmed the players were at the airport waiting to return home, and were also encouraging other teams to pull out of the competition.
"We're waiting for the plane to return to Lome," the Grenoble player told L'Equipe. "We're also talking to the other teams in our group to try to convince them to boycott the competition too."
Togo were due to kick off their campaign against Ghana on Monday.
Manchester City striker Emmanuel Adebayor, who revealed the attack en route to the team's base in the Cabinda province lasted 30 minutes, convened a team meeting as captain on Friday night to discuss whether to stay in Angola or return to their clubs.
The squad now appears to have decided for the latter option, meaning midfielder Moustapha Salifou will be returning to Villa Park.
Togo coach Hubert Velud claimed the authorities should seriously consider whether to call off the whole tournament, although Angola insist their country is committed to hosting a secure competition and said they would step up security.
"We can at least pose ourselves that question," Velud told French radio station RMC this morning. "It's an act of barbarism while we are here to celebrate African football.
"We left the hospital a short time ago to come to the centre for the teams in the competition. We stayed in the hospital a long time so that we could be very united.
"In these situations you become a bit paranoid, you doubt everything.
"We don't feel that the authorities are taking this very seriously.
"I don't mean that they want to hush up the matter, but almost."
Premier League managers have voiced their concerns over security at the tournament.
Hull boss Phil Brown wants his two players participation - Gabon striker Daniel Cousin and Nigerian midfielder Seyi Olofinjana - to return to England.
Brown told The Sun: "I am appalled. This throws a question mark against next summer's World Cup. You simply cannot put the safety of players, officials and fans at the slightest risk. That is totally unacceptable.
"I have two players - Daniel Cousin and Seyi Olofinjana - on duty and I want them back home here with us as quickly as possible."
Tottenham boss Harry Redknapp does not have any players at the tournament but has urged organisers to consider whether it should now go ahead.
Redknapp said: "It's frightening. I agree it's worth considering calling the whole thing off. We can't just sit around and wait for the next shooting."