if your program really reads from STDIN (update: instead of reading the terminal input directly - some unix programs read from /dev/tty for sensitive information, for example)
and the command name really starts with a dash
and you wouldn't try to redirect the output, it might work.
Try this:
my $pwd1 = "pwd1";
my $pwd2 = "pwd2";
open(FOO, "|$command") or die "open command failed: $!";
print FOO "$pwd1\n$pwd2\n";
close FOO;
update 2: redirecting the output shouldn't have any serious consequences, but it may help in that it may show error messages that otherwise might get redirected
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