The 23-year-old striker will instead train individually during Wednesday's training.
In addition to Isak's absence, the national team also announces that goalkeeper Robin Olsen will not participate fully.
During Tuesday's collective training at the Stockholm stadium, Olsen and midfielder Emil Forsberg were missing, where both trained on their own.
- I was hit on the foot last Saturday and have had some swelling.
We have taken it a bit cautiously, but now it feels good, Forsberg said then.
Sweden meets Serbia in Belgrade on Saturday and Slovenia at home at Friends Arena on Tuesday in the Nations League's final group stage matches.
For Sweden, it is important to have Slovenia behind them in the final table to stay in the B division.