Deal was booed by members of his own party as he talked up Tricia Pridemore before the voting.
Everhart received 946 delegate votes at the party convention in Macon on Saturday, defeating Pridemore, who got 755 votes.
Fulton County Republican Party Chairman Shawn Hanley, a former U.S. Marine, dropped out after the first round of balloting.
The race for the volunteer post had become increasingly bitter and had sharply split the Georgia GOP, which had been on something of a high since sweeping statewide elections last year.
Backers credited Everhart, 65, with helping lead the party to historic wins last year. They say she'll keep the party independent.
Supporters of Pridemore argued the 39-year-old former businesswoman possessed the skills to broaden the party's base and make better use of new media. She also wanted to do more outreach to minority groups
Deal's backing of Pridemore created a backlash among some. They said he was trying to strip the party of its independence and make it an extension of the governor's office heading into the 2012 presidential election season.
Deal said Saturday that he has "utmost respect for Sue" and the party needs to reach newcomers.
"I'm grateful that Tricia Pridemore has stepped up," said Deal, and was greeted with a loud and sustained chorus of boos -- along with some cheers.
For Deal, the vote raises questions about how much control he has over his party, particularly the grassroots and tea party factions that lined up behind Everhart. He emerged as the Republican nominee for governor by a slim 2,500-vote margin after a hard-fought runoff last year. Deal is backing Newt Gingrich in the presidential race. But the outcome Saturday suggests he could face obstacles in delivering the state for the former U.S. House speaker.