Instead of foreach, use each with while loops.

Untested:

while( my( $key1, $ref1 ) = each %hash ) {
  while( my( $key2, $val2 ) = each %{$ref1} ) {
    push @Array, { $key2 => $val2 };
  }
}
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Using keys in list context as the expression for a foreach loop is generating a list internally of all of the outer keys, and lists of inner keys. Switching to the while loop saves at least that much.