Villegas accepted an athletic scholarship to attend the University of Florida in Gainesville, Florida, where he played for coach Buddy Alexander's Florida Gators men's golf team in National Collegiate Athletics Association (NCAA) competition from 2001 to 2004. As a freshman in 2001, Villegas was a member of the Gators' 2001 NCAA championship team. During his college golf career, he was the Southeastern Conference (SEC) Freshman of the Year in 2001, the SEC Player of the Year in 2002 and 2004, and an All-American four consecutive years (2001, 2002, 2003, 2004). Villegas graduated from the University of Florida with a bachelor's degree in business administration in 2004.