1. In Magento 2 admin, go to Sales > Orders page, tap on the order which needs partial invoicing.
2. Tap 'Invoice' button at the top of the page. 
3. On the 'New Invoice' page, enter qty 0 for the items which will be invoiced later and leave the qty as is for the items which will be invoice now. Then tap 'Update Qty'.
4. At the bottom this page, ensure 'Amount' dropdown is selected as 'Capture Online' and click on 'Submit Invoice'.
5. This will create the invoice for those items' qty.