The 32-year-old was playing the final one-day international against India on Saturday when he aborted his run-up for the opening delivery of his sixth over before immediately leaving the field.
Watson then failed to appear in his allotted number three slot as Australia's reply began in Bangalore, raising further fears over the injury.
He eventually came in to bat at number eight and, despite several grimaces of pain, managed to battle his way to 49 off just 22 balls, including a hat-trick of sixes.
The player is now expected to undergo further assessment with the opening Ashes Test against England getting under way in Brisbane on November 21.
Limited-overs captain George Bailey was unable to shed any light on the severity of Watson's injury following the game.
"I'm not sure," he said. "He's obviously sore, we saw that.
"We won't know anything until he gets home and gets it properly scanned."