In JSON, arrays [] only every have numeric keys, whereas objects {} have string properties. The inclusion of a array key in your second example forces the entire outer structure to be an object by necessity. The inner objects of both examples are made as objects because of the inclusion of string keys a,b,c,d.

If you were to use the JSON_FORCE_OBJECT option on the first example, you should get back a similar structure to the second, with the outer structure an object rather than an array. Without specifying that you want it as an object, the absence of string keys in the outer array causes PHP to assume it is to be encoded as the equivalent array structure in JSON.

$arrytest = array(array('a'=>1, 'b'=>2),array('c'=>3),array('d'=>4));

// Force the outer structure into an object rather than array
echo json_encode($arrytest , JSON_FORCE_OBJECT);

// {"0":{"a":1,"b":2},"1":{"c":3},"2":{"d":4}}

A JSON array has no explicit indexes, it's just an ordered list. The only JSON data structure that has named keys is an object. The literal should make this quite obvious:

["foo", "bar", "baz"]

This array has no named indices and there isn't any provision to add any.

PHP conflates both lists and key-value stores into one array data type. JSON doesn't.

Try something like this:

//initialize array
$myArray = array();

//set up the nested associative arrays using literal array notation
$firstArray = array("id" => 1, "data" => 45);
$secondArray = array("id" => 3, "data" => 54);

//push items onto main array with bracket notation (this will result in numbered indexes)
$myArray[] = $firstArray;
$myArray[] = $secondArray;

//convert to json
$json = json_encode($myArray);

Try this code

  $users = array();

  $stmt = $mysqli->query('SELECT id, last_active FROM users WHERE status = 1');
  $i=0;
  while ($row = $stmt->fetch_assoc()) {
    $users[$i]['id'] = $row['id'];
    $users[$i]['last_active'] = $row['last_active'];
    $i++;
  }

    echo json_encode($users);

It is do-able, using foreach() loops and exploding the string on the , delimiter.

The below code uses the exact array you supplied above (based on the structure):

foreach($array as $key => &$item) {
    foreach($item as $k => $data) {
        $item = explode(',', $data[0]);
    }
}

Which returns:

[["2","2"],["2","59"]]

Example

If you need the first value as a string and the second as an int, the following should suffice:

foreach($a as $key => &$item) {
    foreach($item as $k => $data) {
        list($string, $int) = explode(',', $data[0]);
        $item = array(strval($string), (int) $int);
    }
}

^{It harnesses the use of strval() to cast the first value as a string and we cast the second value as an int via the (int) loose-typing in PHP.}

Which returns:

[["2", 2],["2", 59]]

Example

A Quick Note

I've used by-reference in the foreach to modify the original array. So basically, you'll fetch your data, run the foreach loops to modify it as you need and then you'll encode it. This is a pseudo example of how that process would go:

ARRAY = Get.ARRAY

FOREACH ( ARRAY AS KEY => &VAL) {
    FOREACH (VAL AS KEY => VALUE) {
        LIST(FIRST_ITEM, LAST_ITEM) = EXPLODE(',', VALUE);
        VALUE = ARRAY ( strval(FIRST_ITEM), (int) LAST_ITEM );
    }
}

ECHO json_encode(ARRAY);

Sure, you could send an array of array. PHP associative array will become a javascript object.

In PHP:

$data = array();
$data['fruits'] = array('apple','banana','cherry');
$data['animals'] = array('dog', 'elephant');
echo json_encode($data);

and then on jQuery

var data = jQuery.parseJSON(response);

then you could then do something like this to access the values

console.log(data.fruits[0]); // apple
console.log(data.animals[1]); // elephant