Can you apply for a PhD that requires an MSc when only 2/3 of MSc grades will be in by application time? I am currently pursuing a Master's in CS in USA. This particular program will only be a year long since I did my undergrad at the same university and had some credits transferred over. I was researching Phd programs in Canada and they all require a Master's degree for admission. I wanted to know if I can apply right now as a Master's student for entry in Fall 2016? 

My program will be over in Spring 2016. My application will contain only 2/3 of my Master's grades by the time of application. I know that you can apply for a Master's program in your last year of undergrad. Is it the same for Phd?
Yes.  When a degree is required prior to starting a program, that degree is needed in order to enrol, but not to apply.