The Brazilian had a banana thrown at him from the stands at El Madrigal, but responded with good humour by picking up the fruit and eating it.
He laughed off the incident in the wake of the game but the Swiss official feels he should not have had to tolerate it.
"What Alves tolerated [on Sunday] is an outratge," he wrote on Twitter.
"We must fight all forms of discrimination united. There will be zero tolerance at the World Cup."
Alves' compatriot and Barca team-mate Neymar took to social media after the match, posting a picture of himself eating a banana and was subsequently joined by many other stars.