Under-20 international Abdi Salaan Mohamed Ali was among eight people killed when a car packed with explosives was detonated at a police station on Monday.
Two other players, Mahmoud Amin Mohamed and Siid Ali Mohamed Xiis, were among 35 people injured.
A militant Islamic group claimed responsibility for the attack.
Blatter wrote to Somali football federation President Said Mahmoud Nur on behalf of FIFA “with a sad heart … having learned of the tragedy.”
Blatter and Nur are scheduled to attend the annual African football congress on Wednesday in Khartoum, Sudan.