Does publishing a manuscript in a respectable journal increase chances of getting a scholarship?
Definitely!  Why 'Masters'? If what you said is true, then aim for a PhD.  I am sure any universities will offer you a scholarship when you wave your marks and paper at them.  

Note: every university has a fixed number of scholarships.  So if one doesn't give you a scholarship, don't be too discouraged. It just means there are students with a better CV than yours.  However, there are many universities and only a very small percentage will have that kind of CV.