In most cases graduate schools don't evaluate graduate student applications as they come in. They usually only admit students once or in some cases twice per year. They application deadline will be in the prior winter for admission in September usually - but this varies by school. So if you put your application in December, they likely won't look at it until just after the deadline - whenever that happens to be. Sometimes you can apply in the summer for winter admission, but not every school does this.
Admissions committees are more interested in the courses that you've taken and how you did in them then when you took them. No one is going to bat an eyelash if you've already taken the standard upper year physics courses and done well in them.
In the end, it's pretty standard for offers of admission to be conditional on successful completion of your degree. So the university will see your final transcripts eventually. It's just that the numbers in your final semester, whenever that is, won't factor into the competitive aspects of the admissions decisions.