I have a MSc degree, want to apply for PhD degree. Should I submit my BSc transcript during admission? I have a BSc and an MSc degree on Computer Science. My BSc CGPA was too low. I somehow got accepted to an MSc degree(two years) and got 4.00 CGPA. I think I am good at my field.

Now I want to apply for a PhD degree, but all universities I checked requires transcripts received from all higher education attended so far.

I don't want to submit my BSc transcript. Is there a way for me to get accepted to a PhD programme without submitting BSc degree? Is there any chance that my MSc transcript override my previous(BSc) degree?
Go ahead and submit your undergraduate transcript.  The admissions committee will be expecting to see one and your application might be screened out before consideration simply because this transcript is missing.  

The fact that you've had good grades in your master's program may help you to overcome the bad impression left by your poor undergraduate GPA.  Having good letters of recommendation and one or more publications (of high quality) will help a lot more.