The started command receives the same STDIN and STDERR from your script, just STDOUT is piped to your script.
You could just close your STDIN before running the command and there will be no input source. Reading from STDIN will cause an error and the called command will exit:
close STDIN;
my @slines = `$command`;
This will also void any chance of console input to your script.
Another approach would use IPC::Open2 which allows your script to control STDIN and STDOUT of the command at the same time:
use IPC::Open2;
open2($chld_in, $chld_in, 'some cmd and args');
print $chld_in "\n\n";
close $chld_in;
@slines = <$chld_out>;
close $chld_out;
This script provides the two \n input needed by the command and reads the command output.