Two-dimensional Array

Situation

So I noticed this is a routine that you will call several times, ie you should update the value of the chairs.

Problems

• As already indicated by the other answers, you are using , instead of ; in the for .
• Your check is if([i][j]) , I do not know which array it is comparing here, I would say a random one.
• You are not adjusting the value of the chair.
• To exit an iteration in javascript it uses return not break .

Code

var cadeiras = [
    [true, false, true, true, true, false, false, true, true, true, false, false],
    [true, false, true, true, true, false, false, true, true, true, false, false], 
    [true, false, true, true, true, false, false, true, true, true, false, false], 
    [true, false, true, true, true, false, false, true, true, true, false, false]
];

function reservar(){
    for (i = 0; i < cadeiras.length; i++){
        for (j = 0; j < cadeiras[i].length; j++) {
            if(cadeiras[i][j]){
                if(confirm("A cadeira " + (j+1) + " na fila " + (i+1) + " está disponível. Deseja reservá-la?")){
                    console.log("A cadeira " + (j+1) + " na fila " + (i+1) + " foi reservada");
                    cadeiras[i][j] = false;
                    return;
                }
            }   
        }
    }
}
reservar();
reservar();

OBS

I would do in an encapsulated function, not to use global variable.

First, correct the syntax of for by replacing , with ;

Then, to exit both loops at the same time, break will not resolve. Encapsulate everything within a function , and when reserving the chair, call return to exit both loops.

function reservarCadeiraDisponivel() {
    for (i = 0; i < cadeiras.length; i++) {
        for (j = 0; j < cadeiras[i].length; j++) {
            if ([i][j]) {
                var reserva = confirm("A cadeira " + (j + 1) + " na fila " + (i + 1) + " está disponível. Deseja reservá-la?");
                if (reserva) {
                    document.getElementById("assento" + numeroCadeira).src = "img/cadeira-tulipa-reservada.jpg"
                    document.getElementById("assento" + numeroCadeira).alt = "reservada"
                    document.getElementById(numeroCadeira).classList.remove("panel-default");
                    document.getElementById(numeroCadeira).classList.add("panel-success");
                    alert("A cadeira " + (j + 1) + " na fila " + (i + 1) + " está reservada.");
                    return;
                }
            }
        }
    }

  alert("Nenhuma cadeira disponível");
  return;
}

The syntax of your for is wrong, if you use ; and not , , I made an example that will return all the values, within if just put the action if the chair is vague:

var cadeiras = [
  [true, false, true],
  [false, false],
  [true]
];

for (i = 0; i < cadeiras.length; i++) {
  for (j = 0; j < cadeiras[i].length; j++) {
    console.log(cadeiras[i][j]);
    if (cadeiras[i][j]) {
      var reserva = confirm("A cadeira " + (j + 1) + " na fila " + (i + 1) + " está disponível. Deseja reservá-la?");
      if (reserva) {
        // faça algo se for reservado.
        return false; // saia do loop.
      }
    }
  }
}

See working at: JsFiddle

It seems like something very simple, here is an example:

Consider that an array traverses the elements through an axis:

+------------------> x
|[true, false, ...]
|[true, false, ...]
|[true, false, ...] 
v
y

To go through javascript, just do something like this, and store the data in an object.

 var cadeiras = [
                 [true, false, true, true, true, false, false, true, true, true, false, false], 
                 [true, false, true, true, true, false, false, true, true, true, false, false], 
                 [true, false, true, true, true, false, false, true, true, true, false, false], 
                 [true, false, true, true, true, false, false, true, true, true, false, false]
                ];
     var free = {"acesso":false};
    for (var y in cadeiras) {
          var x = 0;
          //percorre enquanto for indisponível
          while (cadeiras[y][x] === false) {
            x++; 
          } 
           //sai quando achar o disponível
           free = {"acesso":cadeiras[y][x], "x":x, "y": y}; 
          break;
    }
console.log(free); //a saída será: {acesso: true, x: 0, y: "0"}

Then just display the object:

alert("A cadeira "+free.x+" da fila "+free.y+" está "+((free.acesso) ? 'livre' : 'indisponível')+"!");