You can use LOAD DATA INFILE to bulk load the 800,000 rows of data into a temporary table, then use multiple-table UPDATE syntax to join your existing table to the temporary table and update the quantity values.
For example:
CREATE TEMPORARY TABLE your_temp_table LIKE your_table;
LOAD DATA INFILE '/tmp/your_file.csv'
INTO TABLE your_temp_table
FIELDS TERMINATED BY ','
(id, product, sku, department, quantity);
UPDATE your_table
INNER JOIN your_temp_table on your_temp_table.id = your_table.id
SET your_table.quantity = your_temp_table.quantity;
DROP TEMPORARY TABLE your_temp_table;