eBay spokesman Kevin Pursglove said the company pulled the auction after receiving a letter from the Diallo family's lawyer requesting that it be taken down.
The listing said the door piece included the handle and graffiti paying homage to Diallo. Scheduled to end on May 10, the auction had no bids when eBay closed it.
The auction is the latest controversial or prank listing shut down by eBay. In the wake of the crash of the Mir space station earlier this year, eBay closed some 15 to 20 auctions of Mir debris. Last year, amid the election chaos, eBay closed down an auction of the U.S. presidency.
Diallo died after being hit by 19 of the 41 bullets fired at him. The police officers, who mistook Diallo's wallet for a gun, were acquitted of criminal charges last year.
The seller, Jared November, said in his listing that he planned to give half of the proceeds from the sale of the door fragment to Diallo's family to help them purchase the apartment building where Diallo was shot. Diallo's family has said that they want to buy the building and turn it into a community center.
But Diallo's father said the auction infuriated him and the family wanted no part in the sale of the door.
"We don't need that money," he said.
November salvaged the fragment from the trash last February, he said.
The Associated Press contributed to this report.