Here you go:

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

# NOTE: This program loads all of file1 and file2 into memory, 
#       so if they're huge, this might not work.

my $infile1 = "file1.txt";
my $infile2 = "file2.txt";
#--------------------------------------------------------------------
my %f2 = ();        # KEY=col1, VAL=col2    (in file2)
open my $INFILE2, '<', $infile2 || die "Cannot open \"$infile2\"!\n";
LINE: while(my $line=<$INFILE2>) {
    chomp $line;
    next LINE if($line eq "");      # Skip empties
    my @input = split(/,/, $line);
    $f2{ $input[0] } = $input[1];   # "d" => 90
} #LINE
close $INFILE2;
#--------------------------------------------------------------------
my %f1 = ();
open my $INFILE1, '<', $infile1 || die "Cannot open \"$infile1\"!\n";
LINE: while(my $line=<$INFILE1>) {
    chomp $line;
    next LINE if($line eq "");      # Skip empties

    # Col3=$2, Col5=$3
    if($line =~ m/(\S+, \S+, \S+, (\S+), \S+, (\S+))/) {
        $f1{$2}->{$3} = $1;
    }
    else {
        next LINE;
    }
} #LINE
close $INFILE1;
#--------------------------------------------------------------------
my $outfilename = "output.txt";
open my $OUTFILE, '>', $outfilename;
FILE2COL: foreach my $col1_f2 (keys %f2) {
    next FILE2COL unless (exists $f1{$col1_f2});
    while(my($col5_f1, $line_f1) = each %{ $f1{$col1_f2} }) {
        my $to_match = $f2{$col1_f2};
        print $OUTFILE $line_f1."\n" if( $line_f1 =~ m/$to_match/);
    }
}
close $OUTFILE;
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