Estevao Alberto Gino, 19, who played for Mozambique’s second division club Atletico Mineiro de Tete, lived near the Zambezi river in the western province of Tete.
The incident happened last Thursday.
“On that night, he was training and after jogging he stretched his hands into the water and that was when the crocodile caught him,” coach Eduardo Carvalho told AFP.
Two neighbours who witnessed the attack estimated the crocodile to have been about five-metres (16-feet) long, and “they could not do anything” to save him, said Carvalho.
Crocodile attacks are common along the Zambezi river.
Local police spokesman Leonel Muchina confirmed the incident to AFP saying the footballer’s body has not yet been found.