Two members of the Togo delegation died on Saturday following the ambush in which their bus was sprayed with gunfire on its way to the African tournament which kicks off on Sunday.
The driver of the bus was also killed and several squad members were wounded after the attack in Cabinda province.
Togo said on Saturday they were pulling out of the Nations Cup.
"I have confidence in Africa and it's on the strength of this confidence that we will together organise the flagship competition of world football in 2010," Blatter said in a letter to African Football Confederation (CAF) president Issa Hayatou.
"This terrible incident will not make us forget that African football has written some beautiful pages in the history of world football. It is also the cradle of the pure jewels of football."
This year's World Cup, which starts in June, is being held on the African continent for the first time.
NEWS: Cabinda to still host Nations Cup matches
NEWS: Togo goalkeeper serious but stable
NEWS: Minister - Togo pull out of Nations Cup
NEWS: Manchester City - Adebayor coming home
NEWS: Adebayor - Togo may quit Nations Cup
NEWS: Togo to consult players over pullout
NEWS: Ivory Coast - No plans to quit tournament
NEWS: Organiser - Teams told not to travel by road
NEWS: Jordaan - Gun attack will not affect World Cup
NEWS: African chief seeks Angola security assurances
NEWS: Two of Togo delegation die after ambush
NEWS: Wenger - Nations Cup should continue
NEWS: Nations Cup to continue despite Togo bus attack
NEWS: Togo team bus machine-gunned by rebel soldiers
NEWS: One killed, nine wounded in Togo bus attack
