I have a BCA from Amity(85%), a B.Sc Maths from IGNOU(92%). Both the degrees were begun, and awarded in the same years. Can I go for MS CS ?

No, it requires a four year degree. Eligibility An appropriate four-year bachelor's degree with a final year average of at least mid-B from the University of Toronto or its equivalent another recognized university Applicants from outside Canada are encouraged to submit scores from the GRE G

yes.