Benayoun said after the game that Rodrigo shouted at him: "You are a country of murderers. We'll break your legs."
Shaul Eisenberg, the team's press correspondent, said in response: "The team won't put this on its agenda. We will complain to UEFA."
After the incident, Bosnian referee Siniša Zrnić handed out a yellow card to Benayoun of all people, who was seen arguing with Rodrigo.
Benayoun against Andorra's Vieira (Photo: AP)
Rodrigo denied Benayoun's accusations in a conversation with Ynet.
"Benayoun laughed at us when we were down 0:2 and that's why he got a yellow card," said the Andorran coach. "The fourth ref said this to the head ref. I never said any sentence like this to him. And what we said between us is nothing important, it was football talk."
Afek added: "We did our part. I'm glad we completely dominated the game, making it an easy game. The goal scored on us was unnecessary. You can count on one hand the number of times Andorra made it past the half line."
Tomer Ganor contributed to this report