This works for me:

$item = ['qty' => 11]; // For example
$product->setStockData(['qty' => $item['qty'], 'is_in_stock' => $item['qty'] > 0]);
$product->save();

Edit:

This is no longer the correct way to handle this, because $product->save() is deprecated since Magento 2.1. The correct way to do this is by using the StockRegistryInterface:

/**
 * @var StockRegistryInterface
 */
protected $stockRegistry;

/**
 * Inventory constructor.
 * @param StockRegistryInterface $stockRegistry
 */
public function __construct(
    StockRegistryInterface $stockRegistry
)
{
    $this->stockRegistry = $stockRegistry;
    parent::__construct();
}

With the above code, you can use the following:

$sku = 'ABC123';
$qty = 10;
$stockItem = $this->stockRegistry->getStockItemBySku($sku);
$stockItem->setQty($qty);
$this->stockRegistry->updateStockItemBySku($sku, $stockItem);

Use Managers as much as possible. Keep your modules decoupled from each other. It's The Magento Way™

This works for me:

$item = ['qty' => 11]; // For example
$product->setStockData(['qty' => $item['qty'], 'is_in_stock' => $item['qty'] > 0]);
$product->save();

Edit:

This is no longer the correct way to handle this, because $product->save() is deprecated since Magento 2.1. The correct way to do this is by using the StockRegistryInterface:

/**
 * @var StockRegistryInterface
 */
protected $stockRegistry;

/**
 * Inventory constructor.
 * @param StockRegistryInterface $stockRegistry
 */
public function __construct(
    StockRegistryInterface $stockRegistry
)
{
    $this->stockRegistry = $stockRegistry;
    parent::__construct();
}

With the above code, you can use the following:

$sku = 'ABC123';
$qty = 10;
$stockItem = $this->stockRegistry->getStockItemBySku($sku);
$stockItem->setQty($qty);
$this->stockRegistry->updateStockItemBySku($sku, $stockItem);

Use Managers as much as possible. Keep your modules decoupled from each other. 

It's The Magento Way™

This works for me:

$item = ['qty' => 11]; // For example
$product->setStockData(['qty' => $item['qty'], 'is_in_stock' => $item['qty'] > 0]);
$product->save();

This works for me:

$item = ['qty' => 11]; // For example
$product->setStockData(['qty' => $item['qty'], 'is_in_stock' => $item['qty'] > 0]);
$product->save();

Edit:

This is no longer the correct way to handle this, because $product->save() is deprecated since Magento 2.1. The correct way to do this is by using the StockRegistryInterface:

/**
 * @var StockRegistryInterface
 */
protected $stockRegistry;

/**
 * Inventory constructor.
 * @param StockRegistryInterface $stockRegistry
 */
public function __construct(
    StockRegistryInterface $stockRegistry
)
{
    $this->stockRegistry = $stockRegistry;
    parent::__construct();
}

With the above code, you can use the following:

$sku = 'ABC123';
$qty = 10;
$stockItem = $this->stockRegistry->getStockItemBySku($sku);
$stockItem->setQty($qty);
$this->stockRegistry->updateStockItemBySku($sku, $stockItem);

Use Managers as much as possible. Keep your modules decoupled from each other. It's The Magento Way™