Ok I saw a couple of things..

1) In your code you incremented your value even though the first line doesnt match "/\./". So you always start at 2 instead of 1.
2) you were using sprintf for your output when perl already had what you wanted to do built in via the nifty 'x' operator...

I also changed the var names, just cause I could :)
So here is what I came up with

#!/usr/local/bin/perl -wT

use strict;

my($putNum,$line,$s_count,$num,$n_line, @square);

$putNum = 1;

@square = (
   '+----+',
   '|....|',
   '|....|',
   '|....|',
   '+----+'
);

foreach $line (@square) {

   if (!$putNum) {
      $line =~ s/\./ /g;

   } else {

      if ($line =~ /\./) {
         $s_count = $line =~ s/\./\./g;

         $num++ if ($s_count);

         $n_line = "$num" . ' ' x ($s_count - length($num));

         $line =~ s/\.+/$n_line/o;
      }
   }

   print "$line\n";
}

# OUTPUT

+----+
|1   |
|2   |
|3   |
+----+
[download]

Is this what you were looking for? The same number of spaces that were previously '.'s on the line?

Happy Hackin :)

/* And the Creator, against his better judgement, wrote man.c */