The answer is Yes, but the “Ship all items” button is disabled.
Because when stock equal or less than 0, it means that you don’t have items at that moment to ship to customers.
Note: You have to allow backorders shipping with a product first here
Step 1: Complete order as normal. The order is still in “Processing” status.
Step 2: When you have items to ship, select Order history > Take shipment button to ship to the customer and complete the order.