This code

@newList[@newOrder] = @list;

Means:-

$newList[1] receives $list[0] which is 'zero'
$newList[3] receives $list[1] which is 'one'
$newList[4] receives $list[2] which is 'two'
$newList[0] receives $list[3] which is 'three'
$newList[2] receives $list[4] which is 'four'

whereas this code

@newList = @list[@newOrder];

Means:-

$newList[0] receives $list[1] which is 'one'
$newList[1] receives $list[3] which is 'three'
$newList[2] receives $list[4] which is 'four'
$newList[3] receives $list[0] which is 'zero'
$newList[4] receives $list[2] which is 'two'