Fernandez, the 2013 National League Rookie of the Year, signed for $635,000, a franchise high for a player coming off his rookie season.
Fernandez was compensated for being an All-Star, Rookie of the Year, finishing third in the Cy Young Award voting and twice being Pitcher of the Month.
Yelich, who became the everyday left fielder in late July, signed for $505,000.
The MLB minimum is $500,000.
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter