"Everything looks like it's nothing major. There's no telling on how he's going to feel tomorrow," Murphy said.
It's too soon to tell if Upton will be able to play in Thursday's series finale against the Brewers or during the series against the Dodgers beginning Friday to end the regular season.
Upton wasn't available after the game for comment.
Upton was pursuing Logan Schafer's opposite-field ball down the left-field line, when it appeared as if he lost his footing just as he reached the padded fence, with his head hitting the padding.
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.
• Injured finger ends Kemp's season early
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.