You will need an import file that contains the new price and the variation SKU. For this process to work correctly, your products will need to have unique SKUs.
- Create an "Existing Items" import to WooCommerce Products: https://d.pr/i/c5daMc
- On Step 3 of the import process, leave the Product Type set to Simple and add the new price information: https://d.pr/i/P6XQhC
- On Step 4 of the import process, select to match on the custom field _sku and add the SKU element from your import file: https://d.pr/i/7EwWTl
- Also on Step 4, select to update the custom fields _price, _regular_price and _sale_price only: https://d.pr/i/gaXjgl