Ah, ok, that was originally not clear from the question. You can use split to get the list from the string:

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

my %hash1 = (key1 => 'val1,val2',
             key2 => 'val3',
             );
my %hash2 = (val1 => 'val5,val6,val7',
             val2 => 'val8,val9',
             val3 => 'val3',
            );
my %result = map { $_ => join ',', map split(/,/, $hash2{$_}),
                                       split /,/, $hash1{$_}
                 } keys %hash1;

while (my ($k, $v) = each %result) {
    print "$k: $v\n";
}
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