Vargas did start the 2005 season with Greensboro, as was expected, but he advanced quickly through the Marlins' minor-league system. He made five starts with Greensboro, going 4–1 with an earned run average of just 0.80 in five starts and was named South Atlantic League Pitcher of the Week on April 24, and the Marlins Organizational Pitcher of the Month for April, and Minor League Player of the Week honors for the week of April 18–24. He was then promoted to Jupiter, where he went 2–3 with a 3.42 ERA in nine starts; while there, he struck out 60 batters in 55 innings. With his third club of the year, the Double-A Carolina Mudcats, he made three starts, going 1–0 with a 2.84 ERA and 25 strikeouts in 19 innings pitched. He led all Florida minor league pitchers in 2005 with a 2.50 ERA.