Estudiantes said Jesus Quintero was injured by flying glass when stones were thrown at the bus by rival fans, breaking windows, following the match away to Llaneros de Guarane.
Photographs showed that the 18-year-old player, who had scored his first professional goal in his team's previous match, suffered a cut around his eye as well as injuries to his lips and hands.
The club said the operation was a success and Quintero would not suffer long-term damage.
The Venezuelan Football Union (AUFP) described the incident in the town of Guarane as "deplorable".
"We hope that the relevant authorities take action over these type of incidents which continue to stain our football," said the association on Twitter.
Llaneros won the match 3-1 in the Clausura championship, the second stage of the Venezuelan season.