You already have gotten working but let me tell 'tear apart' your code, to tell you what went wrong. You should see this as a chance to learn, no offence meant.

I put some comments into your sourcecode, always above the line which they belong to:

# good, open with error checking
opendir(DIR, "$dir") || die "can't open $dir $!\n";

# maybe name the variable @filenames - as there is more than one
# or get rid of the variable altogether by saying
# foreach my $oldname ( readdir(DIR) )
my @filename = readdir (DIR);

# declare filename with my and give better name (see above)
# foreach my $oldname (@filename)
foreach $filename (@filename) { 

  # this matches against the special variable $_
  # (which you are not using) you want
  # if ($filename =~ / /)
  if (/ /) {  
    
    # the regex is completely wrong you want either
    # s/ +/./g or tr/ /./ try to figure out the difference
    # and $newfile is never assigned a value so:
    my $newfile = $oldfile;
    $newfile =~ s/ +/./g;

    # you don't have to do the rename when you didn't
    # change anything, so
    rename($oldname, $newfile) unless $oldname eq $newfile;
  }
}
closedir(DIR);
[download]

If you want to use this as a standalone script, I'd go for the rename program out of the Cookbook (recipe 9.9):

#!/usr/bin/perl -w
# rename - Larry's filename fixer
$op = shift or die "Usage: rename expr [files]\n";
chomp(@ARGV = <STDIN>) unless @ARGV;
for (@ARGV) {
    $was = $_;
    eval $op;
    die $@ if $@;
    rename($was,$_) unless $was eq $_;
}
[download]

which can be used e.g. in the following ways (also from the Cookbook)

% rename 's/\.orig$//'  *.orig
% rename 'tr/A-Z/a-z/ unless /^Make/'  *
% rename '$_ .= ".bad"'  *.f
% rename 'print "$_: "; s/foo/bar/ if <STDIN> =~ /^y/i'  *
% find /tmp -name '*~' -print | rename 's/^(.+)~$/.#$1/'
[download]

This approach has several advantages, as you can specify the affected files from the command line (and don't have to work on all files in a directory). Furthermore it is very flexible due to the eval approach. Your problem could be solved with it like this:

% rename 's/ +/./g'  *
or
% rename 'tr/ /./' *
[download]

Try to understand how this program works - and if you have any questions, feel free to ask here ...

-- Hofmator