The signed 18-inch-by-24-inch artwork depicts part of a blue American flag and includes the words "God," "one nation," and "with liberty and justice for all" printed in the stripes.
It was posted on the auction site by Mr Zimmerman on the morning of Monday, December 16, and sparked a bidding frenzy.
The first offer was for a mere $0.99 but within a day the bidding had reached an astonishing $99,999.
The painting eventually went for $100,099.99 when the auction closed at 9.55am on Saturday.
The unknown buyer was one of 24 people who put in a total of 96 bids for what Mr Zimmerman says was his "first hand-painted artwork".
In his eBay listing he added: "Everyone has been asking what I have been doing with myself. I found a creative, way to express myself, my emotions and the symbols that represent my experiences.
"My art work allows me to reflect, providing a therapeutic outlet and allows me to remain indoors :-) I hope you enjoy owning this piece as much as I enjoyed creating it. Your friend, George Zimmerman."
Mr Zimmerman was accused of profiling, following and shooting Trayvon, 17, a guest in a gated development in Sanford, Florida as the teenager was returning from a trip to a local convenience store.
The 30-year-old claimed self-defence and was acquitted by a six-person jury earlier this year, a verdict which sparked nationwide protests.
Since his acquittal Mr Zimmerman has had several brushes with the law including being stopped twice for speeding, in Texas and Florida.
In September, he was questioned by police after his estranged wife called 911 saying he threatened her with a gun. He was not charged over the alleged incident, which occurred a week after she filed for divorce.
In November, Mr Zimmerman was arrested on domestic violence charges, which were later dropped after his girlfriend withdrew her complaint.
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