The South African Football Association has reported that Meyiwa was shot and killed in what is reported to be a robbery in Vosloorus in the East Rand, Johannesburg, on Sunday, 26 October.
In his letter to South African Football Association (SAFA) president Danny Jordaan, Hayatou said words alone could not express the sadness caused by Senzo's demise.
"It is with shock and dismay that CAF has learnt about the passing away of South Africa and Orlando Pirates captain and goalkeeper Senzo Meyiwa. Losing such a talented player and young gentlemen is a tragedy for South African and African football, and our thoughts are with his family and relatives," Hayatou said.
"Meyiwa was one of the most promising South African players and he took with great pride and responsibility his role as Captain of both the national team and his club Orlando Pirates. Words cannot express enough our sadness."
"In my personal name, on behalf of the CAF Executive Committee and the entire African football family, we present to the family of the deceased, to SAFA, to Orlando Pirates and to all those who knew Meyiwa our deepest condolences," Hayatou said.