The Colombia international suffered an injury against Liverpool, while David Alaba and Thiago picked up knocks just days before they take on BVB
James Rodriguez will have further tests on an injury scare on Wednesday after he was forced off during Bayern Munich's Audi Cup clash with Liverpool.
Bayern 21/20 to beat BVB
The Colombia star was withdrawn in the second half of the 3-0 loss to Jurgen Klopp's side at the Allianz Arena after complaining of discomfort and headed straight down the tunnel.
James' injury came after Thiago was forced off with abdominal pain, while David Alaba was taken off with 11 minutes left after picking up a problem of his own.
Head coach Carlo Ancelotti is not worried about the knocks to Thiago or Alaba but he confirmed that James will have a check-up on a muscular problem.
"Thiago and Alaba both took hits," Ancelotti said. "It's no big problem."
He added on James: "We'll investigate it [on Wednesday]."
The injuries were a low point during a dismal 90 minutes for Bayern, who were soundly beaten by Liverpool thanks to goals from Sadio Mane, Mohamed Salah and Daniel Sturridge.
The Bundesliga champions have lost four of their last five pre-season games, including a penalty shoot-out defeat to Arsenal following a 1-1 draw, and confidence is low ahead of the DFL-Supercup meeting with Borussia Dortmund on Saturday.
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Bayern meet Napoli in the Audi Cup third-place play-off on Wednesday in a match that could give some players some much-needed extra game time, although Ancelotti has ruled out risking Arjen Robben or Jerome Boateng, who both sat out Tuesday's game.
"They will not play [on Wednesday]. We don't want to take any risks. They're not yet ready," he said.