Thousands of fans were waiting Sunday night at Lome's airport, where the team was greeted by Prime Minister Gilbert Houngbo, the BBC reported.
The crowd watched quietly with many people in tears as the coffins bearing the two members of the delegation killed in the attack were carried across the runway.
Houngbo called it a "sad day" and a "disgrace for African football". The prime minister ordered the team's return home and sent a government plane to Angola to fly it back to the capital.
The Togolese delegation's bus came under fire Friday from separatists in the oil-rich Angolan province of Cabinda.
The bus driver, assistant coach Abalo Amnalete and team spokesman Stanislas Ocloo died in the attack. Goalkeeper Kodjovi Obilale was taken to intensive care in South Africa to receive treatment for gunshot wounds.
A minute's silence for the victims was held before the opening game in Luanda Sunday. Angolan President Jose Eduardo dos Santos condemned the attack in his opening speech but said Cabinda would remain one of the cup's venues.
The province is separated from the rest of Angola by around 40 kilometres of territory belonging to the Democratic Republic of Congo.
The Togolese were due to face Ghana's national team, known as the Black Stars, Monday evening.