The Civic bested four other finalists, which included the Volkswagen Passat with a diesel engine, The Detroit News reported Friday.
The Passat was named the Motor Trend Car of the Year on Thursday.
Finalists also included the Toyota Prius V, the Ford Focus Electric and the Mitsubishi i, the News said.
"This, to Honda, is everything," said Michael Accavitti, vice president of marketing for American Honda Motor Co.
"Environmental awareness is right in our wheelhouse," he said.
Rob Cogan, editor of the Green Car Journal, said the honor, for Honda, was overdue.
"There is no other vehicle like the Civic Natural Gas on American highways, and this recognition has been a long time coming for Honda," Cogan said.