Everton suffered their second straight loss without any reply this season which sent them bottom of the Premier League table.
Onana discovered afterwards that racist messages had been sent his way on social media.
Everton have released a statement expressing their disgust, with an investigation already underway to find the perpetrators.
The statement read: “Everton Football Club strongly condemns any form of racist and discriminatory abuse towards our players.
“The club is aware of a racist post targeted at Amadou Onana. Such abuse is vile and will not and should not be tolerated.
“The club is conducting an investigation to identify the individual responsible and will also be supporting police with any investigation they conduct.
“We must all take a zero-tolerance stance by reporting such behaviour to social media platforms and the authorities. Racism has no place online, in our stadia or in our communities.”
Belgium international Onana joined Everton from Lille last season and made 33 Premier League appearances in his debut season in England.