In the ninth inning, Lobaton hit a ground ball to Milwaukee first baseman Jace Peterson, who flipped the ball to Josh Hader, covering the bag. Hader appeared to miss the base and fell to the ground.
Hader reached for the bag with his glove, beating a lunging Lobaton. The Cubs backstop tripped while avoiding a collision with the Brewers closer, tumbling to the ground and landing on his right shoulder.
"I know it's pretty serious," manager David Ross said of Lobaton. "He was in some real pain."
Ross guessed Lobaton separated the shoulder, adding the 36-year-old will undergo x-rays.
Tony Wolters will likely join the Cubs for a third stint on Wednesday. The Cubs designated him for assignment in mid-May, and after he went unclaimed on waivers, outrighted him to Triple-A Iowa.
The Cubs will have to make a 40-man roster move to add Wolters.
Lobaton is the fourth backup catcher the Cubs have used this season behind Willson Contreras, who leads MLB in innings caught, and third to go down with an injury.
Austin Romine hasn't played since April due to a wrist sprain. P.J. Higgins will soon undergo flexor tendon repair surgery, ending his season.
Top prospect Miguel Amaya, another catcher on the 40-man roster currently playing with Double-A Tennessee, is on the minor-league injured list with a forearm strain.