Yes, you can still earn points! Please note, though, that the amount of points you earn will correspond with your actual total (amount paid), not the item's original price.
An item costs ¥10,000. If you ordered this item and did not use any points, you would earn 100 points for your purchase.
However, if you use 2,500 points on your order, the item's new total will come out to ¥7,500. This means you will earn 75 points for your order.