Upton was able to retrieve the ball and throw it back to the infield as Schafer settled for a triple.
Upton remained on his back for several minutes before leaving with his arm wrapped around a trainer for support.
Travis Jankowski entered the game in right field with Wil Myers sliding over from right field to left field after Upton's departure.
Upton entered the game against the Brewers hitting .251 this season with a team-high 26 home runs to go with 81 RBIs.
Earlier Wednesday, the team announced that right fielder Matt Kemp would not play in the final five games of the regular season after suffering a partially torn tendon in his right middle finger.