Try the below code. This works even if you have comma more than once in a line.
Code:
use strict;
use warnings;
while(<DATA>) {
s/\"(.*?)\,(.*?)\"/$1.$2/ge;
print;
}
__END__
"ro,han",rahul,kunal,"sw,ati"
rohan,"r,ahul","kun,al",swati
rohan,"rah,ul",kunal,swati
"ro,han",rahul,kunal,"s,wati"