The team's assistant coach and spokesman died of wounds sustained when the bus they were travelling in came under attack on Friday in Cabinda province, an oil-rich region separated from the rest of Angola by a thin strip of Democratic Republic of Congo.
An Angolan bus driver was killed at the scene.
'Mourning the dead'
As he boarded the plane, Emmanuel Adebayor, Togo's captain, told journalists: "We have to mourn our dead. We go back home to do this."
The players earlier said that the team had decided at a meeting late on Saturday that they would line up against Ghana in the first match of the tournament in tribute to the dead.
"People died for this tournament, others were injured. We can't abandon them and leave like cowards," Alaixys Romao, a Togo midfielder, was quoted as telling France's L'Equipe newspaper.
"Our government doesn't necessarily agree with us but we are determined to play in this competition. The decision was taken unanimously."
Thomas Dossevi, a Togolese striker who plays for the French side Nantes, echoed Ramo's remarks saying that the team would line up against Ghana for their first game of the tournament "in memory of the dead".
"We are all heartbroken, it is no longer a party, but we want to show our national colours, our values and that we are men," he said.
Witnesses said that the squad was seen training for Monday's scheduled game on Sunday morning.
'Attacks will continue'
The Africa Cup of Nations got under way on Sunday in the Angolan capital, Luanda, with a game between the hosts and Mali. Seven matches of the three-week tournament were due to take place in Cabinda.
The Confederation of African Football (CAF), the tournament organisers, said in a statement on Saturday that all the matches would go ahead as scheduled.
A group fighting for the independence of the oil-rich region, which is divided from the rest of Angola by Democratic Republic of Congo, claimed responsibility for the attack on Friday, saying it was aimed at the team's military escorts.
Rodrigues Mingas, the secretary-general of The Forces for the Liberation of the State of Cabinda-Military Position (Flec-PM) said the group would continue its attacks against Angolan targets.
"This attack wasn't against the Togolese it was against the Angolan occupation forces. We have nothing against Togo. We are supporting and admire their players a great deal," he told Al Jazeera from Luxembourg.
"We are not killers. Two months ago we wrote to the Confederation of African Football president, Issa Hayatou. On his desk he has our letters warning that there was a risk in organising the tournament in Cabinda.
"Cabinda is not Angola, we have no common border with Angola, our languages are different, we are from different tribes, we have nothing to do with them. They are occupying our country for the black gold."
Samuel Petrequin, a sports writer for The Associated Press news agency, told Al Jazeera that the streets of Cabinda were "peaceful" in the wake of the attack.
"It seems the games will go ahead as planned," he told Al Jazeera.
"There is no violence at all, maybe they can have the games as it was planned. The Angolan government said after the attack that it was going to increase security measures."
Al Jazeera's Mourad Labarab, reporting from Cabinda, said that security measures had become "very tight".
"The army have been deployed throughout the city and also we have seen checkpoints ... movement in the city has become very difficult and just getting close to the stadiums could take hours.