The Brazilian international will be replaced by former Russia captain Alexey Smertin as one of the draw assistants for Saturday's event in St Petersburg, FIFA said in a statement, adding that Hulk had withdrawn due to club commitments.
Zenit are away to FC Ural on Sunday in a Russian Premier League match, although there have been no alterations to the fixture list since FIFA initially announced on Wednesday that Hulk would take part in the draw.
The World Cup's local organising committee said the decision was made purely on sporting grounds by Zenit coach Andre Villas-Boas.
"Very recently, we found out that the coach of Zenit made a decision based on purely sporting reasons to withdraw this player from taking part in the draw show," Chief Executive Alexey Sorokin told a news conference.
"I reiterate that this decision was purely of a sporting nature because Zenit has a game on Sunday in Yekaterinburg, so the coach decided the team need to leave together, not leaving anyone behind."
Other former players who will take part in Saturday's draw include Ronaldo (Brazil), Diego Forlan (Uruguay), Fabio Cannavaro (Italy), Samuel Eto'o (Cameroon) and Oliver Bierhoff (Germany).
Russia, hosts for the 2018 World Cup, have repeatedly been criticised for failure to tackle racism in domestic soccer.
Hulk had said he was honoured after being named as a draw participant on Wednesday.
"I'm happy," he said. "I am honored to participate in this ceremony, which will officially begin the path to the next World Cup. I have quite adapted to life in Russia, and my family really like St Petersburg."
However, on Monday, he had complained bitterly about racism in Russian football.
"It (racism) happens at almost every match in Russia but the world does not hear about it because they try to keep it quiet," Hulk told reporters on Monday at a Zenit training session.
"I see it happening all the time. I used to get really angry about it but now I just send a kiss to the fans and try not to get angry."
The problem was again brought under the spotlight when Ghanaian Emmanuel Frimpong said he was racially abused in a match at Spartak Moscow.
Frimpong, who plays for Ufa, was sent off, and later suspended for two league matches after raising a finger to fans who he said had made monkey chants.
On Wednesday, the Russian Football Union (RFU) rejected the racism allegations, a ruling Frimpong said was "beyond a joke".
(Editing by Sudipto Ganguly)
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