How can I connect in Dubai if the UAE won't let me transit because of my nationality?

According to a Timatic search using the United Airlines interface, you can transit without a visa.

Searching for a Afghan national transiting in the Emirates yields:

United Arab Emirates - Transit Visa

Visa required.

Transiting without a visa is possible for:

Holders of confirmed onward tickets for a max. transit time of 24 hours.

Visa is required for transit between Dubai International Airport (DXB) and Dubai Al Maktoum International (DWC).

So if you have an onward ticket for a transit under 24 hours, and you don't need to change airports, you're fine.

BTW, even Israelis, who certainly can't get a visa for Dubai (without very special circumstances), can transit there without a visa, and routinely do so.

You don't need a visa to transit, as long as your transit is less than 24 hours - yours is 12 hours so no issues there.

You can spend time airside in the large transit lounge. There is a hotel, plenty of shopping and places to relax, eat and even take a shower if you so please.

You won't be boarded if you are not eligible for transit, so there is no risk of being "stuck".

Relax, and enjoy your trip.