Something like this?

#! perl -slw
use strict;
use Data::Dumper;

my @array = ( [0,1],[2,3],[4,5],[6,7]);
my @compare = (2,4,5,6);

@array = map{ $array[$_] if $array[$_][1] != $compare[$_] } 0..$#array
+;

print Dumper \@array;
[download]