fssize=$(df -k $fs | grep -v Filesystem | awk \'{print $2}\');

Same as:

fssize=$(df -k --output=size $fs);

(but probably a little slower that this last line...)

've tried and backticks and qx// and IPC::Run, and even open() but they all seem to have the same limitation - when I pass the hash element as the command to be executed it gets interpreted one line at a time

thus forget about the for loop, forget about the bash array and do all in one line

 perl -e 'my $foo=`df -k --output=size /tmp /var /home`; $foo=~s/\n//g
+; print "$foo\n";' 
returns --> 1K-blocks   12345  67890 1234567890
[download]

You can now manipulate the string $foo directly in perl