Monday's decision disappointed the oil refining industry which has also complained E15 can damage engines in boats, outdoor equipment, and older cars.
"The Supreme Court's decision denies the petitioners their day in court and will have negative repercussions for consumers," said Charles Drevna, the president of the American Fuel and Petrochemical Manufacturers industry group.
Ethanol groups applauded the rejection of the challenge. The decision clears the way for more fuel options for U.S. drivers, said Jeff Lautt, the CEO of POET, one of the world's largest ethanol producers. "We think drivers deserve reliable choices at the pump," he said.
Automotive News and Bloomberg contributed to this report.