The issue with your regular expression is that you are capturing the first number, not the second, into your buffer. You could get your expected result modifying your regular expression to not capture the first digits:

#!/usr/bin/perl
use strict;
use warnings;

my @data = grep $_, <DATA>;

print sort RowSort @data;

sub RowSort {

    my($aa) = $a =~ /\d+,(\d+)/;         
    my($bb) = $b =~ /\d+,(\d+)/;         
        
    $aa <=> $bb;       
}



__DATA__
1,64,1.4.5,1.4.6,44642850,44642850,0,27348,10028,59188,1488095,761904.
+64
1,128,1.4.5,1.4.6,25337850,25337850,0,19236,10276,28196,844595,864865.
+28
1,256,1.4.5,1.4.6,13489200,13489200,0,17792,11372,17832,449640,920862.
+72
1,512,1.4.5,1.4.6,6996270,6996270,0,18084,16744,19124,233209,955224.06
+4
1,1024,1.4.5,1.4.6,3557880,3557880,0,31528,20488,35188,118596,971538.4
+32
2,64,1.4.5,1.4.6,44642850,44642850,0,25828,9548,40128,1488095,761904.6
+4
2,128,1.4.5,1.4.6,25337850,25337850,0,27936,10796,28696,844595,864865.
+28
2,256,1.4.5,1.4.6,13489200,13489200,0,12852,10692,13332,449640,920862.
+72
2,512,1.4.5,1.4.6,6996270,6996270,0,17184,15904,18844,233209,955224.06
+4
2,1024,1.4.5,1.4.6,3557880,3557880,0,34068,17948,36628,118596,971538.4
+32
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Using YAPE::Regex::Explain to parse the regex:

The regular expression:

(?-imsx:\d+,(\d+))

matches as follows:
  
NODE                     EXPLANATION
----------------------------------------------------------------------
(?-imsx:                 group, but do not capture (case-sensitive)
                         (with ^ and $ matching normally) (with . not
                         matching \n) (matching whitespace and #
                         normally):
----------------------------------------------------------------------
  \d+                      digits (0-9) (1 or more times (matching
                           the most amount possible))
----------------------------------------------------------------------
  ,                        ','
----------------------------------------------------------------------
  (                        group and capture to \1:
----------------------------------------------------------------------
    \d+                      digits (0-9) (1 or more times (matching
                             the most amount possible))
----------------------------------------------------------------------
  )                        end of \1
----------------------------------------------------------------------
)                        end of grouping
----------------------------------------------------------------------
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See perlretut.