It would be really bad if Perl started treating the contents of variables as Perl code. Use Data::Diver.

#!/usr/bin/perl

use strict;
use warnings;

use Data::Diver  qw( DiveVal );
use Data::Dumper qw( Dumper );

my %hash;
my @keys = ( 5, 6 );

# $hash{root}...{2} = 'b';
DiveVal( \%hash, map \$_, 'root', @keys, 2 ) = 'b';

print Dumper(\%hash);
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Tip: For best results, always pass a scalar to Dumper. If you want to dump an array or hash, pass a reference to it.