Older cars were "never designed to use E15," spokeswoman Gloria Bergquist said. Use of the fuel over time could create significant engine problems, she said.
The API cites engine problems discovered during a study it commissioned last year, but the Energy Department called the research flawed and said it included engines with known durability issues.
For now, E15 remains a regional anomaly. About 20 stations currently offer the fuel in Illinois, Iowa, Kansas, Nebraska, South Dakota and Wisconsin.
Dinneen and other ethanol advocates said the Supreme Court ruling may serve as a breakthrough for E15, after years of delay.
"With this decision, E15 can finally become a meaningful option for more Americans," Dinneen said.