Garcia finished ahead of France manager Didier Deschamps and St Etienne coach Christophe Galtier to win the award.
The 49-year-old, who is in his first season at Roma, has led the Giallorossi to break a club record of 15 straight games without losing in Serie A.
A statement from France Football read: "Following an excellent coaching debut in Serie A, Roma coach Rudi Garcia has been chosen as the best French coach of the year."
Garcia, who won the same award back in 2011 after leading Lille to a French double - Ligue 1 title and the Coupe de France - could not believe the news.
"I honestly didn't expect this," Garcia told France Football. "Fortunately, I was sitting down when I heard the news.
"I was pleasantly surprised by the announcement."
Roma are second in Serie A, three points behind leaders Juventus.