Results were released Tuesday by the People for the Ethical Treatment of Animals.
Underwood, 24, a Grammy-winning country singer, won the title in 2005. Eubanks, 49, leader of NBC's "Tonight Show" band, is a newcomer to the winner's circle.
Eubanks leapt ahead of his competitors with help from Jay Leno, who encouraged viewers to vote for Eubanks and "bring honor" to the late-night NBC talk show.
"I'm gonna keep this campaign going," Leno said during a recent show after sharing a photo of a shirtless Eubanks with his audience. Leno said the shot, in which Eubanks is holding a backpack and posing against a woodsy backdrop, wasn't doctored.
Runners-up in the contest, which the animal rights group said drew more than 110,000 votes on its Web site, included Joaquin Phoenix, Milo Ventimiglia, Kristen Bell, Bryce Dallas Howard, Jared Leto and Lisa Edelstein.
Last year, Prince and Bell, who starred on the "Veronica Mars" TV series, were picked as the two sexiest vegetarians. Previous winners also include Natalie Portman, Andre 3000, Coldplay's Chris Martin, Shania Twain, Tobey Maguire, Lauren Bush, Josh Hartnett and Alicia Silverstone.