The Padres announced that Tatis exited because of a shoulder subluxation, which is a partial dislocation of the joint, and will undergo an MRI on Tuesday.
Padres manager Jayce Tingler told reporters that Tatis has experienced minor dislocations in the past but said that Monday's incident was the most pain he's ever seen Tatis in. Tingler also acknowledged that the nagging shoulder issue may have been bothering Tatis "more than we realized."
Tatis crumpled to the ground in pain after swinging and missing at a 2-2 pitch from San Francisco's Anthony DeSclafani in the third inning, leaving Petco Park in silence. He walked off the field with assistance from Tingler and a trainer, cradling his left arm against his body.
"Of course it's concerning," Tingler said. "You don't want to see him have to play through injury, pain, any of those things, or lack of strength or range of motion. Again, we don't want to jump the gun on anything; hoping for good news and kind of see where it goes from there."
Tingler said he believes Tatis' shoulder popped out on the field and was put back in place in the training room.
"It comes out, it comes back in, so he's been dealing with that," Tingler said. "Obviously tonight was the first time we've seen it in game action from swinging or anything like that."
Tatis, 22, left a game late in spring training with left shoulder discomfort after making a backhand play but was back two days later. Tingler said then that Tatis had been dealing with left shoulder discomfort since his minor league days. Tatis later said he'd had it since rookie ball.
Earlier in the spring, Tatis was shaken up while sliding headfirst into home and missed several games.
Tatis has struggled through the first five games, batting just .167 and committing five errors, although he hit a 465-foot home run Sunday in a loss to Arizona. He signed the longest contract in big league history on Feb. 22, a 14-year, $340 million deal.
If Tatis is sidelined for an extended period, Tingler said San Diego's "first option" at shortstop would be rookie Ha-Seong Kim, who replaced Tatis on Monday. Jake Cronenworth, Jorge Mateo and Tucupita Marcano also potentially could play shortstop.
The Associated Press contributed to this report.