Swansea City Cameron Toshack
The Swans, which started with a mix of youth and experience of four recognised first-team and seven development players, lost 3-0 at Kingsmeadow Stadium in their Group B clash.
Despite chances from Owain Jones and Marvin Emnes it was the home side who capitalised through a first-half strike from winger Andy Barcham before a brace from midfielder Dom Poleon secured a convincing win for Wimbledon.
"It was a disappointing defeat but the game is a valuable learning experience for our young players," said Toshack. "The idea of a competition like this is that our younger players learn from the experience and develop against experienced professionals.
"Wimbledon were a very competitive League One side who gave us a tough game. We battled well against them in the first half and were unlucky to go in a goal down at the break.
"We struggled to impose ourselves in our attacking play, which is something we have been very good at in recent weeks while our decision-making cost us."
The Swans included eight Under-23 players in their starting XI alongside the first-team experience of Emnes, Franck Tabanou and Gerhard Tremmel.
Despite the defeat, Toshack insisted the Swans still have a chance to progress in the competition with League Two sides Newport and Plymouth still to play.
"We have belief we can progress," he added. "It has been a good test for our younger academy players against League One opposition.
"Wimbledon were competitive and physical - some have never played at this level before, but this is the level we now know to expect.
"Tonight is a valuable learning experience. It is what games like this are all about and we know we need to come back stronger next time."