In front of a healthy crowd, Argyle could have gone behind in the opening 30 seconds when Laura Low was put through but shot straight at Michaela Phillips.
Argyle looked nervous from the start as they failed to string any decent passes together, with Wimbledon controlling the early exchanges. The visitors were unlucky to have a third minute goal disallowed for offside.
The lively Ezme Wells then saw her effort blocked with a dangerous corner from Kayleigh Brown being desperately touched away by goalkeeper Suaneu Salgado. Argyle were slowly getting into the game with Wells shooting over and Brown firing straight at Salgado.
The Pilgrim defence were coping well with the visitors until they conceded a needless free-kick in the 36th minute on the edge of the penalty area, which Sami Bock fired home. Argyle hit back with Salgado saving well from Wells, before Becky Atkins shot narrowly wide.
Argyle came out for the second half determined to get back into the game and almost drew level when Natasha Knapman put in Wells, who saw her stunning strike hit the top of the crossbar. Brown made way for Dani Barr who made an immediate impact when her shot was saved.
Unfortunately, nine minutes into the second half, a fast break ended with Low converting a right-wing cross for a 2-0 Wimbledon lead.
Wells was by now terrorising the visitors defence and her dangerous cross to Knapman almost resulted in a goal. Amber Pollock came on for Izzy Berks to boost the attack but the home defence were once again caught out by a fast break with the ball going to Low, who made no mistake with the finish.
Phillips then pulled off a great save as Wimbledon looked to increase their lead. Argyle threw everything into the attack with Marks having a shot blocked and Pollock's follow up shot being superbly saved by Salgado.
Marks had another effort blocked before seeing another effort expertly saved with Barr also denied by the outstanding Salgado. It was Wells who epitomised Argyle’s disappointing afternoon when, after being put through by Atkins, her thunderous drive rebounded of a post. Argyle kept pushing for a goal but it never came and they were out of the competition.
Argyle manager Dave Leonard was in reflective mood after the match: “Unfortunately, it was three personal defending errors that cost us dear, although great credit must go to the Wimbledon goalkeeper as she stopped everything we threw at her.
“We didn't get going in the first half and we suffered from basic defensive errors. I felt we got on the front foot in the second half but hitting the woodwork twice and being denied by an outstanding goalkeeper summed up our performance.”