Pompey collected eight points to top their group, while their opponents finished second in Group C with five points to their name.
Match preview
Portsmouth, who won the EFL Trophy in 2018-19, are competing in the knockout rounds after winning two and drawing one of their three group matches.
After playing out a goalless draw with Fulham in their opening match, Pompey won the subsequent penalty shootout to claim the bonus point, before they went on to ease to a 5-1 win against Gillingham and a 2-1 victory over Leyton Orient.
As well as enjoying success in the EFL Trophy, John Mousinho's side are currently sitting top of the League One table after racking up 48 points from 21 matches.
Pompey extended their lead to seven points with a comfortable 3-0 victory over Shrewsbury Town on Saturday thanks to an Abu Kamara brace and a Marlon Pack strike - a result that represents their fourth consecutive victory without conceding.
They will now put their promotion bid on hold to focus on Tuesday's home fixture, where they will try to reach the last 16 of the EFL Trophy for the seventh consecutive season.
Wimbledon, meanwhile, will appear in the knockout rounds for a second straight campaign after finishing behind Wycombe Wanderers in the top two of Group C.
After beating Stevenage on penalties to take a bonus point from their first match, they went on to claim a 2-0 win over Crystal Palace under-21s.
Although they lost out to Wycombe in their final group game, Wimbledon did enough to set up a midweek trip to Fratton Park, where they will look to continue their fine spell of form after winning two and drawing one of their last three matches.
Johnnie Jackson's charges claimed comfortable wins over Ramsgate and Swindon Town in the FA Cup and League Two respectively, before they played out a goalless draw in Saturday's away meeting with Salford City to leave them in the final playoff place in League Two.
Although they took a useful point from the weekend's contest, the draw leaves them without a win in six away matches since beating Harrogate Town on October 3.
Portsmouth EFL Trophy form:
W
W
W
Portsmouth form (all competitions):
D
L
W
W
W
W
AFC Wimbledon EFL Trophy form:
W
W
L
AFC Wimbledon form (all competitions):
L
W
L
W
W
D
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Team News
Pompey are still unable to call upon Regan Poole, Conor Ogilvie, Anthony Scully, Tom Lowery and Tino Anjorin due to injury.
Defender Sean Raggett is set to serve a one-match suspension after being sent off in Portsmouth's most recent EFL Trophy fixture against Leyton Orient,
With the fixtures coming thick and fast, Mousinho will take the opportunity to make a number of changes, with the likes of Zak Swanson, Ryley Towler, Ben Stevenson, Christian Saydee and Gavin Whyte all expected to get rare starting opportunities.
As for the visitors, Nikola Tzanev is set to replace former Pompey goalkeeper Alex Bass after featuring between the posts in all three group games.
Jackson is likely to rotate his squad for the trip to the South Coast, which could result in Alex Pearce, Isaac Ogundeere, James Tilley and James Ball.
After scoring two goals in the group phase, forward Josh Davison is also set to return to the starting lineup for Tuesday's contest.
Portsmouth possible starting lineup:
Schofield; Swanson, Towler, Shaughnessy, Hume; Stevenson, Jewitt-White; Saydee, Devlin, Whyte; Bishop
AFC Wimbledon possible starting lineup:
Tzanev; Ogundere, Pearce, Johnson, Currie; Tilley, Little, Ball, Lemonheigh-Evans; Davison, Bugiel