James went off just before half-time, with the Colombia international showing few signs of pain as he exited the field.
There were initial suspicions he was withdrawn due to a knock to the head, having looked dazed shortly beforehand after getting struck by the ball.
But Bayern confirmed after the game that the on-loan Real Madrid midfielder felt his calf tighten.
And, following investigations from Bayern's medical team on Wednesday, they have come to the conclusion he should only need to miss "a few days of training".
A club statement read: "Bayern midfielder James was not seriously injured in yesterday's [Tuesday] Champions League game against Besiktas.
"An in-depth investigation confirmed the first diagnosis of the club doctor. The Colombian has only slight problems in the muscles of the left calf and thus has to miss a few days of training."