Richarlison was the target of a banana thrown from the crowd as Brazil thrashed Tunisia 5-1 in a friendly in Paris on Tuesday, while Neymar edged closer to Pele's all-time scoring record for the five-time world champions.
The game at the Parc des Princes was also briefly paused in the first half as the crowd were twice implored not to point laser pens at Brazil players.
"Unfortunately... a banana was thrown on the pitch towards Richarlison, scorer of the second Brazilian goal," the Brazilian football confederation (CBF) said on Twitter.
"The CBF reinforces its position to combat racism and repudiates any prejudiced act."
The Selecao produced a dominant first-half display in their final outing before travelling to Qatar for the World Cup, with Raphinha netting twice and Neymar moving to within two of Pele's record.
Richarlison also found the net, while Pedro scored as a second-half substitute before responding to more boos and missiles from the crowd by bowing in front of them in celebration.
"It's a shame, it's difficult to see images like that," said Brazil captain Thiago Silva, whose team posed for a team photo before the match with a banner bearing an anti-racism message.
"Unfortunately it seems that we can't change people's mentality.
"I hope they will realise that this doesn't work, it's the past, we have to change. Unfortunately, people continue with this mentality."
Tite's Brazil will head into their World Cup Group G opener against Serbia on November 24 on a 15-match unbeaten run, dating back to their Copa America final loss to Argentina last year.
The scene for a bad-tempered match was set when the vast numbers of Tunisia fans jeered the Brazilian national anthem before kick-off.
"I was puzzled, I was saying 'No, it's a lack of respect'. Football is a sport that promotes inclusion," said Tite.
Brazil took the lead in the 12th minute, though, as Casemiro clipped the ball over the top and Barcelona winger Raphinha directed a wonderful looping header over Tunisia goalkeeper Aymen Dahmen and into the net.
Jalel Kadri's men hit back six minutes later.
Defender Montassar Talbi met Anis Slimane's out-swinging free-kick to send a powerful header into the bottom corner past 'keeper Alisson.
Incredibly, Brazil were back ahead just seconds after that setback, as Raphinha sent Richarlison in behind to drill a strike through the legs of Dahmen to score his third goal in two games after a double against Ghana.
The Tottenham forward celebrated in front of the Tunisian supporters, who responded by throwing a banana and plastic cups in his direction.
Fred kicked the banana off the pitch before extra security guards took up residence on the side of the field.