Store string into int[] array

You may use

int intrect = Integer.parseInt(rect[j]);

to convert your rect[j] to int.

public static void main(String[] args) {
    // TODO Auto-generated method stub

    String strings = "100.122.323.344;543.433.872.438;218.544.678.322";
    strings = strings.replace(".", ",");
    System.out.println(strings);
    String[] coordinates = strings.split(";");
    String[] rect = null;
    int[][] intcoordinates = new int[3][4];  // initialize the size of the array
    for (int i = 0; i < coordinates.length; i++) {
        // System.out.println(coordinates[i]);
        rect = coordinates[i].split(",");        
        for (int j = 0; j < rect.length; j++) {
            intcoordinates[i][j] = Integer.parseInt(rect[j]);
        }
    }
}

intcoordinates contains [[100, 122, 323, 344], [543, 433, 872, 438], [218, 544, 678, 322]] at the end of the execution. This is the final result of the conversion.

Initialize a two dimentional array intcoordinates with rows and cols. If don't know the row size, than you should count maximum row size. Than convert String to int and assign to this array.

 int[][] intcoordinates=new int[coordinates.length][countMaxRow(coordinates)];
 for(int i=0;i<coordinates.length;i++){
    rect= coordinates[i].split(",");
    for(int j=0;j<rect.length;j++){
       intcoordinates[i][j]=Integer.parseInt(rect[j]);
    }
 }
 System.out.println(Arrays.deepToString(intcoordinates));

Here is maximum row count method

static int countMaxRow(String[] arr){
    int max=0;
    for (String str : arr) {
        String a[]=str.split(",");
        if(max< a.length){
            max= a.length;
        }
    }
    return max;
}

Conceptually Scanner and collections should work for you:

        String strings = "100.122.323.344;543.433.872.438;218.544.678.322";
    Scanner scanner = new Scanner(new ByteArrayInputStream(strings.getBytes()));
    scanner.useDelimiter(";");
    List<List<Integer>> list = new ArrayList<>();

    while(scanner.hasNext())
    {
        Scanner scanner2 = new Scanner(new ByteArrayInputStream(scanner.next().getBytes()));
        scanner2.useDelimiter("\\D");
        List<Integer> lst = new ArrayList<>();
        while(scanner2.hasNextInt())
            lst.add(scanner2.nextInt());
        list.add(lst);  
    }
    System.out.println("Lists: ");
    for(List<Integer> lst : list)
        System.out.println(lst);