The Frenchman was named as leader in Arkéa-Samsic's line-up on Tuesday but on Wednesday morning the team announced he would not start.
"Following recent events, Nacer Bouhanni is not in the condition to start Scheldeprijs," read the short statement.
On Monday, Bouhanni revealed he had been subjected to racist abuse online following his disqualification from the Cholet-Pays de la Loire for an irregular sprint that forced Jake Stewart into the barriers.
He posted screenshots of some of the hateful messages he'd received, which included references to his Maghreb heritage.
On Tuesday, he expanded on the issue in an emotional interview with L’Equipe, saying he'd been suffering for 25 years and that the "incessant" abuse of the past week was "the last straw".
He has confirmed he will file a complaint with French police.
Bouhanni's withdrawal from Scheldeprijs follows his near-withdrawal from Sunday's La Roue Tourangelle in France.
"I told the team manager [Emmanuel Hubert] that I couldn't do it anymore, that psychologically I couldn't go to the Roue Tourangelle," Bouhanni said, revealing he'd just had an argument with his father over the recent issues.
"My father told me to go and race, whilst I was still taking stock of everything. He told me not to pay attention, not to read these things. Manu Hubert as well. And when I received the call-up for the Roue Tourangelle, I said to myself, 'it feels like no one is listening to me, that no one understands me."
Bouhanni went to the race after all and finished second behind Arnaud Démare.
On Wednesday, shortly before Arkéa-Samsic announced Bouhanni would not start the final Classic of the Flemish spring, the UCI issued a statement in support of the French sprinter.
Last Monday, the governing body announced it had opened disciplinary proceedings in relation to the Cholet incident, saying it 'firmly condemns' Bouhanni's deviation and would 'demand the imposition of sanctions' by its Disciplinary Commission.
On Wednesday, it said: "The Union Cycliste Internationale (UCI) wishes to firmly condemn the racist attacks aimed at the French rider Nacer Bouhanni on social media.
"However serious the fault of the French rider – which forced the UCI to refer the incident to its Disciplinary Commission and demand the imposition of sanctions against him – , nothing justifies the insults he has been subject to in the days following the act he is accused of."
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