Thome, 41, has dealt with back issues for the past several years. He's listed as day to day.
He came into the game batting .118 with 10 strikeouts in 17 at-bats this season before grounding out and walking in two plate appearances Saturday night.
He was replaced at first base by Ty Wigginton in the top of the fifth.
Thome was injured sliding into second base breaking up a double play in the fourth. Phillies manager Charlie Manuel admitted that Thome's history of back issues raised some red flags.
"That's very concerning [since he's had back problems in the past]," Manuel said.
"In the American League, that's why they kept him in a DH role. I always thought when he played in the field he dove a lot because he didn't have what you'd call real great range, so balls hit close to him he'd usually dive. And he's kind of heavy, so when he hit it, he'd kind of jar [his back]. He's a big man, and it takes its toll over the years."
Thome tried to remain optimistic.
"I've had this in the past; I haven't had it this year. Any time you come out of a game, sure, you get concerned. Absolutely," Thome said. "It kind of accumulated during the game. I could kind of feel it getting stiff. And then when I slid into second base and got up, that's when I really felt it. Hopefully it will clear up quick."
He conceded, though, that he needs to get more at-bats to get out of his slump, and he obviously can't do that if he's sidelined.
"That part of it is frustrating, because you do want to get out there and you do want to play and then this happens," Thome said. "I think the key is to stay positive and be a good teammate and get here as early as you can and get in there and get your treatment."
Paul Hagen is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.