You can use IPC::Open3 or a "piped open" , to open your shell, then print commands to it, by printing to the filehandle. There are plenty of examples around, like:

my $pid=open3(\*IN,\*OUT,0,'/bin/sh');
# print to and read from IN and OUT
#
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or

open(CHILD, "| ./myscript 2>&1") or die "Can't open: $!";
print CHILD "mycommand\n";
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There is alot of fine tuning that you need to do depending on the shell you are opening, like whether you need to print a newline after each command.