Please, specify - do you need to delete those product which you have in your .csv file or all the products that you have except of those which are in the .csv file?
If you need to delete exactly those products which you have in your .csv file, then as I know via import it is not possible. But you can set specific mark for those products, lets say set those products you want to delete as out of stock or set quantity for them 0, in this way they will be not seen in the front-end. Then you can filter all out-of-stock products and delete them in bulk.
In case you have other products which are out of stock, beside of those you would like to delete, then you can do in some other way - in Excel you can add to names of products you would like to delete the word “delete” and import the file. Then you will be able to filter the products by the name - all containing the word Delete will be filtered. Then select them and remove in bulk.
You can do the mentioned via admin, but it will take some time as it may require server resources. You can do it also via Store Manager for Magento application, it will save you some time as there you can import applying changes on a fly without file modification and create custom filter.
In any case 2-weeks free version available for download -
In case you need to delete all the products except of those which are in the .csv file, using the mentioned application you will be able to do that, since there is an option “Delete products which are not in .csv”