Alonso, who has been battling back stiffness, had a bone scan, and it revealed something more serious: a stress reaction in his lower back. He won't be joining the team on its trip to San Francisco, where the Padres open a three-game series on Friday.
"There's an absolute possibility he doesn't play again this season," assistant general manager Josh Stein said.
Alonso, who is hitting .282, left the Padres' game on Sept. 1 with lower back tightness. All indications are that was his final appearance this year. While Alonso's average is tops among Padres regulars, he has just five home runs and 31 RBIs in 103 games.
Upton's ailment isn't as serous, as he had two ingrown toenails removed on Thursday.
"He's a little sore," Padres interim manager Pat Murphy said.
Upton, though, was available to pinch-hit in Thursday's finale against the Rockies. Murphy said Upton will play the majority of games going forward. But his absence on Thursday had Wil Myers playing left field for the first time.
"I've never played left field in the big leagues," Myers said. "I'll just play left field like it is right field."
Right field is where Myers had most of his experience before coming to the Padres from the Rays. But this spring, Myers was asked to learn a new position -- center field -- and spot in the batting order -- leadoff.
Myers, who has been bothered by a wrist injury this year, also started eight games at first base, to go with his 32 in center.
He returned on Friday from his latest stint on the disabled list. He's hit .261 (6-for-23), which includes three hits in Wednesday night's 11-4 win over the Rockies.
"I feel good," he said. "It's just good to be back on the field. I'm still trying to find that consistent approach each and every at-bat."
Jay Paris is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.