It's because Perl is interpolating variables into your string, use single quotes instead:
system('paste Output1.txt Output2.txt | awk \'{print $1, $2, $5, $15}\'');
or:
system(q(paste Output1.txt Output2.txt | awk '{print $1, $2, $5, $15}'));
in any case, it is better to do this all in Perl without using system
for increased performance, readability, and portability.