You could read the entire input line from scanner, then split the line by , then you have a String[], parse each number into int[] with index one to one matching...(assuming valid input and no NumberFormatExceptions) like

String line = scanner.nextLine();
String[] numberStrs = line.split(",");
int[] numbers = new int[numberStrs.length];
for(int i = 0;i < numberStrs.length;i++)
{
   // Note that this is assuming valid input
   // If you want to check then add a try/catch 
   // and another index for the numbers if to continue adding the others (see below)
   numbers[i] = Integer.parseInt(numberStrs[i]);
}

As YoYo's answer suggests, the above can be achieved more concisely in Java 8:

int[] numbers = Arrays.stream(line.split(",")).mapToInt(Integer::parseInt).toArray();  

To handle invalid input

You will need to consider what you want need to do in this case, do you want to know that there was bad input at that element or just skip it.

If you don't need to know about invalid input but just want to continue parsing the array you could do the following:

int index = 0;
for(int i = 0;i < numberStrs.length;i++)
{
    try
    {
        numbers[index] = Integer.parseInt(numberStrs[i]);
        index++;
    }
    catch (NumberFormatException nfe)
    {
        //Do nothing or you could print error if you want
    }
}
// Now there will be a number of 'invalid' elements 
// at the end which will need to be trimmed
numbers = Arrays.copyOf(numbers, index);

The reason we should trim the resulting array is that the invalid elements at the end of the int[] will be represented by a 0, these need to be removed in order to differentiate between a valid input value of 0.

Results in

Input: "2,5,6,bad,10"  
Output: [2,3,6,10]

If you need to know about invalid input later you could do the following:

Integer[] numbers = new Integer[numberStrs.length];
for(int i = 0;i < numberStrs.length;i++)        
{
    try 
    {
        numbers[i] = Integer.parseInt(numberStrs[i]);
    }
    catch (NumberFormatException nfe)   
    {
        numbers[i] = null;
    }
}

In this case bad input (not a valid integer) the element will be null.

Results in

Input: "2,5,6,bad,10"  
Output: [2,3,6,null,10]

You could potentially improve performance by not catching the exception (see this question for more on this) and use a different method to check for valid integers.

Use int which converts a string to an int, inside a list comprehension, like this:

desired_array = [int(numeric_string) for numeric_string in current_array]

Suppose, for example, that we have a arrays of strings:

String[] strings = {"1", "2", "3"};

With Lambda Expressions ^{[1] [2]} (since Java 8), you can do the next ▼:

int[] array = Arrays.asList(strings).stream().mapToInt(Integer::parseInt).toArray();

▼ This is another way:

int[] array = Arrays.stream(strings).mapToInt(Integer::parseInt).toArray();

—————————
Notes
  1. Lambda Expressions in The Java Tutorials.
  2. Java SE 8: Lambda Quick Start

Use array_map i.e.

$array = array_map(function($n) { return (int)$i; }, $array);

Given an array you can use the Array.ConvertAll method:

int[] myInts = Array.ConvertAll(arr, s => int.Parse(s));

Thanks to Marc Gravell for pointing out that the lambda can be omitted, yielding a shorter version shown below:

int[] myInts = Array.ConvertAll(arr, int.Parse);

A LINQ solution is similar, except you would need the extra ToArray call to get an array:

int[] myInts = arr.Select(int.Parse).ToArray();