Swindon made 6 changes to the starting line up from the side that beat Port Vale at the weekend, with Phil Smith starting in goal, along with Devera, Risser, Connell, Kerrouche, and De Vita.
Swindon took the lead mid way through the second half with a 30 yard shot from outside the box from Risser to make it 1-0 on 68 minutes.
On 82 minutes AFC Wimbledon equalised, which ended Swindon's run on clean sheets, that had lasted for 5 1/2 games. The AFC Wimbledon goal was a header scored by Yussuff from close range.
With no extra time being played in the Johnstone's Paint Trophy the game finished 1-1 and went straight to a penalty shoot out.
Phil Smith saved AFC Wimbledon's first, second, and fourth kicks, with the third finding the back of the net.
Meanwhile Swindon only needed to take 3 of their 5 penalties, which were all scored by Connell, Risser, and Esajas to put Swindon into Saturday's semi final draw.