Indeed. All you need is the -i option, and possibly the -p option (see perlrun) to do the loop and the printing. You can even use them in regular scripts. Note that with the -p option, anything you want to do before the loop needs to be in a BEGIN block.

In the next code, the -l option takes care of the newlines.

#!/usr/bin/perl -p -i.bak -l
BEGIN {
    @ARGV = 'personel.txt';
    $newdigit="+615";
    $id="0001";
}
if(/^$id\|/o) {
    my($id, $name, $family, $oldphone) = split /\|/;
    $newphone = $newdigit .$oldphone;
    $_ = join ("|", $id, $name, $family, $newphone);
}
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p.s. You're trying to read from a file opened for append. Jeez.