The Bees had to work hard for it, having gone two goals behind early on.
Jamie Stephens was back from injury, and made an early save to prevent further goals.
On 44 minutes, Dan Sweeney broke for the Bees, and some neat attacking play saw Justin Amaluzor get in front of his marker to slot home just before half time.
After the break, some good Bees combination play led to the next goal on 60 minutes, as Wesley Fonguck scored to make it 2-2.
And a few minutes later, Tobi Coker pulled the Bees in front with his snap shot catching AFC Wimbledon unawares.
The Bees had to ride it out against the wind for last 20 minutes, as AFC Wimbledon made the game very direct.
But the Bees hung on to see out the win and book themselves a spot in the final.
They will now take on Bristol City in the final, with details to be confirmed soon.
The U23’s are in action again here at the Hive tomorrow when they take on Nike Academy at 1pm.