There is no "pass by reference" available in JavaScript. You can pass an object (which is to say, you can pass-by-value a reference to an object) and then have a function modify the object contents:

function alterObject(obj) {
  obj.foo = "goodbye";
}

var myObj = { foo: "hello world" };

alterObject(myObj);

alert(myObj.foo); // "goodbye" instead of "hello world"

You can iterate over the properties of an array with a numeric index and modify each cell of the array, if you want.

var arr = [1, 2, 3];

for (var i = 0; i < arr.length; i++) { 
    arr[i] = arr[i] + 1; 
}

It's important to note that "pass-by-reference" is a very specific term. It does not mean simply that it's possible to pass a reference to a modifiable object. Instead, it means that it's possible to pass a simple variable in such a way as to allow a function to modify that value in the calling context. So:

 function swap(a, b) {
   var tmp = a;
   a = b;
   b = tmp; //assign tmp to b
 }

 var x = 1, y = 2;
 swap(x, y);

 alert("x is " + x + ", y is " + y); // "x is 1, y is 2"

In a language like C++, it's possible to do that because that language does (sort-of) have pass-by-reference.

edit — this recently (March 2015) blew up on Reddit again over a blog post similar to mine mentioned below, though in this case about Java. It occurred to me while reading the back-and-forth in the Reddit comments that a big part of the confusion stems from the unfortunate collision involving the word "reference". The terminology "pass by reference" and "pass by value" predates the concept of having "objects" to work with in programming languages. It's really not about objects at all; it's about function parameters, and specifically how function parameters are "connected" (or not) to the calling environment. In particular, note that in a true pass-by-reference language — one that does involve objects — one would still have the ability to modify object contents, and it would look pretty much exactly like it does in JavaScript. However, one would also be able to modify the object reference in the calling environment, and that's the key thing that you can't do in JavaScript. A pass-by-reference language would pass not the reference itself, but a reference to the reference.

edit — here is a blog post on the topic. (Note the comment to that post that explains that C++ doesn't really have pass-by-reference. That is true. What C++ does have, however, is the ability to create references to plain variables, either explicitly at the point of function invocation to create a pointer, or implicitly when calling functions whose argument type signature calls for that to be done. Those are the key things JavaScript doesn't support.)

Function arguments are like new variable assignments, it's not like references or pointers in C. It's more something like this:

function testFunc(...args) {
  var outTestArray = args[0];
  var aiTemp = [1,2,3,4];

  /*Using slice(0) to clone array */
  outTestArray = aiTemp.slice(0);
}
...

As you can see, in the code above you are cloning the array and assigning it the variable outTestArray scoped within the function, which is not accessible outside of it.

You could use a closure to achieve what you want:

var outerArray;
function testFunc(array) {
  var aiTemp = [1,2,3,4];
  outerArray= aiTemp.slice(0);
}

or even better, just return a new array:

function getArray() {
  return [1,2,3,4];
}

var aiTest = getArray();
...

const args = ['p0', 'p1', 'p2'];
call_me.apply(this, args);

See MDN docs for Function.prototype.apply().

If the environment supports ECMAScript 6, you can use a spread argument instead:

call_me(...args);

Arrays in JS are objects and are passed into functions by value, where that value is a reference to the array. In other words, an array passed as an argument to a function still points to the same memory as the outer array.

This means that changing the array contents within the function changes the array passed from outside the function.

function f(arr) {
  arr.push(1); 
  return arr;
}

var array = [];

// both function calls bellow add an element to the same array and then return a reference to that array. 

// adds an element to the array and returns it.
// It overrides the previous reference to the array with a 
// new reference to the same array.
array = f(array);
console.log(array); // [1]

// adds an element to the array and ignores the returned reference.
f(array);
console.log(array); // [1, 1]

First thing is arrays are always passed as reference in javascript.

Now coming to your question, when an array is passed to a function the argument variable of that function will hold that reference, in your case it's arr argument. If you mutate arr it will mutate original array as it is referring to original array but if you just assign some other value or reference to arr it will no longer hold reference to that original array and any changes to new reference won't have any effect on that array.

When you do:

citiesNames = [];
citiesPos = [];

the variables are no longer references to the original arrays that were passed in, now they're references to these two empty arrays.

If you want to clear out the original arrays, you can simply set their lengths:

citiesNames.length = 0;
citiesPos.length = 0;

Inside your function there's this:

funcArray = new Array();
funcArray = someArray;

This won't actually copy someArray but instead reference it, which is why the original array is modified.

You can use Array.slice() to create a so-called shallow copy of the array.

var funcArray = someArray.slice(0);

Modern versions of ES also support destructuring expressions, which make it look like this:

const funcArray = [...someArray];

The original array will be unaltered, but each of its elements would still reference their corresponding entries in the original array. For "deep cloning" you need to do this recursively; the most efficient way is discussed in the following question:

What is the most efficient way to deep clone an object in JavaScript?

Btw, I've added var before funcArray. Doing so makes it local to the function instead of being a global variable.