Yet another (more perl-ish) way to do it :

my @a = (1,2,3,4,5,6); 
my @b=(1,5,3,6,8,2,4);
my %aref = map {$_=>\$_} @a;
my $cand;  # Candidate value to replace the selected value
exists ($aref{$_}) or $cand=$_,last  for @b;
${$aref{3}}=$cand; # Assuming you want the value "3" replaced 
print @a;
#--Output --
#128456
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