Other answers create a new copy of the array, if you want to modify the array in place you can use:
arr.splice(_.findIndex(arr, { id: 3 }), 1);
But that assumes that the element will always be found inside the array (because if is not found it will still remove the last element). To be safe you can use:
var index = _.findIndex(arr, { id: 3 });
if (index > -1) {
arr.splice(index, 1);
}