% perl -0015 -pe chomp infile > outfile

# or even better
% perl -0015 -pe 's{^\cZ$}{}; chomp' infile > outfile


# deparse shows that -l0 cannot work

% stephan@ape (/c/cygvar/tmp) %
% perl -MO=Deparse -l0 -0015 -pe1               
BEGIN { $/ = "\r"; $\ = "\000"; }
LINE: while (defined($_ = <ARGV>)) {
    chomp $_;
    '???';
}
continue {
    print $_;
}
-e syntax OK

# checking

% stephan@ape (/c/cygvar/tmp) %
% echo abc def | xargs -n1 | perl -lpe '$_.="\cM"' | cat -evnt
     1  abc^M$
     2  def^M$

% stephan@ape (/c/cygvar/tmp) %
% echo abc def | xargs -n1 | perl -lpe '$_.="\cM"' | perl -0015 -pe chomp | cat -evnt
     1  abc$
     2  def$