Harper finished with 112 points, while Miley earned 105.
Miley, who led the D-backs with 16 wins and a 3.33 ERA, struck out 144 batters in 194.2 innings of work.
The 20-year-old Harper hit .270 with 22 home runs and 59 RBI for the first-place Nationals. He also stole 18 bases.
The left-hander made the team out of spring training but did not join the starting rotation until April 23, where he shutout the Phillies on two hits over six innings of work.
Miley was also the team's representative in the All-Star Game in Kansas City.