Use an index for your array of fields, combined with the /g modifier. This one works:

#!/usr/bin/perl -w
use strict;
my $line =
    "00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,00,00,00,"
   ."02,00,01,00,39,00,39,00,39,00,39,00,30,00,30,00,30,00,30,00,"
   ."00,00,00,00,00,00,00,00,00,00,";

my @fields = (100, 101, 102, 103);

my $index =0;

$line =~ s/\b39\b/$fields[$index++]/g;

print $line;
__END__
output:
00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,01,00,00,\ 
00,02,00,01,00,100,00,101,00,102,00,103,00,30,00,30,00,30, \
00,30,00,00,00,00,00,00,00,00,00,00,00,
[download]

See perlre for an explanation of the modifiers I have used here.