I have completed my M.C.A degree in two years, instead of three. Am I eligible to apply for an M.S. in the U.S.A?

I have a total of 17 years of study( B.C.A + M.C.A),but, I took admission directly into the second year of M.C.A through lateral entry. Does skipping the first year of my 3- year Masters degree affect my eligibility to get into a US university?

Your eligibility is dependent on the awarded degree and its equivalence to US degree. You must be eligible if you have degree from a good school. You can always check with the school you plan to apply, if you want to be sure.