If they have a VAT number prefixed “EU” then that means they’re a non-EU supplier of electronic services that charges consumers in the EU at their respective local rates of VAT using the “MOSS” scheme. Although this VAT has been charged at the UK rate it is not UK VAT and you can’t reclaim it on your VAT return.
MOSS only applies to consumer sales, not business-to-business. If you are VAT registered then you need to provide your VAT number to the supplier, and they will be able to invoice you without charging you any VAT at all. You pay the supplier without VAT, but you have to make a special “reverse charge” declaration on your VAT return.
For this particular invoice, if you can’t get the supplier to retrospectively change it from a consumer sale (MOSS VAT) to a business one (zero VAT, reverse charge) then I’m afraid all you can do is enter it in QuickFile with the total purchase value in the net column including the non-reclaimable VAT, and the VAT rate set as “no VAT”. For future purchases from the same supplier you need to tell them you’re a business and get them to invoice you without VAT in future. If you have any kind of online account or “control panel” type thing for the supplier then there will probably be an option somewhere in your account settings to give them your VAT number, or just email them and ask for advice.
If you mean you’ve already submitted a VAT return where you mistakenly claimed back the VAT on this purchase then you should probably credit note the original purchase (that you recorded at 20% VAT) and then create another purchase at no VAT as I described above. This will reduce your box 4 claim for this quarter by the amount you over-claimed last time. As long as the difference is under £10,000 then that should be all there is to it (https://www.gov.uk/vat-corrections).